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molecular evolution

Graham M Hughes, Emma M Boston, John A Finarelli, William J Murphy, Desmond G Higgins, Emma C Teeling
The olfactory receptor (OR) gene families, which govern mammalian olfaction, have undergone extensive expansion and contraction through duplication and pseudogenization. Previous studies have shown that broadly-defined environmental adaptations (e.g terrestrial vs aquatic) are correlated with the number of functional and non-functional OR genes retained. However, to date, no study has examined species-specific gene duplications in multiple phylogenetically divergent mammals to elucidate OR evolution and adaptation...
March 19, 2018: Molecular Biology and Evolution
Josphat K Saina, Zhi-Zhong Li, Andrew W Gichira, Yi-Ying Liao
Ailanthus altissima (Mill.) Swingle (Simaroubaceae) is a deciduous tree widely distributed throughout temperate regions in China, hence suitable for genetic diversity and evolutionary studies. Previous studies in A. altissima have mainly focused on its biological activities, genetic diversity and genetic structure. However, until now there is no published report regarding genome of this plant species or Simaroubaceae family. Therefore, in this paper, we first characterized A. altissima complete chloroplast genome sequence...
March 21, 2018: International Journal of Molecular Sciences
Marta Florio, Michael Heide, Anneline Pinson, Holger Brandl, Mareike Albert, Sylke Winkler, Pauline Wimberger, Wieland B Huttner, Michael Hiller
Understanding the molecular basis that underlies the expansion of the neocortex during primate, and notably human, evolution requires the identification of genes that are particularly active in the neural stem and progenitor cells of the developing neocortex. Here, we have used existing transcriptome datasets to carry out a comprehensive screen for protein-coding genes preferentially expressed in progenitors of fetal human neocortex. We show that fifteen human-specific genes exhibit such expression, and many of them evolved distinct neural progenitor cell-type expression profiles and levels compared to their ancestral paralogs...
March 21, 2018: ELife
Tara A Pelletier, Robert D Denton
Reproductive isolation is the result of either the inability to produce viable and fertile offspring or the avoidance of mating altogether. While these mechanisms can evolve either over time via genetic drift or natural selection, the genetic result is usually a complex set of traits that are often linked. Explaining how reproductive isolation proceeds from the initiation of divergence to the complete prevention of mating is often a difficult task, as the underlying genes for traits associated with reproductive isolation can change via molecular evolution and subsequent protein coding alterations or through alterations of gene expression regulation...
January 2018: Molecular Ecology
Surinder Pal Kaur, K S Sujith, C N Ramachandran
The replacement of methane (CH4) from its hydrate by a mixture of nitrogen (N2) and carbon dioxide (CO2) involves the dissociation of methane hydrate leading to the formation of a CH4-N2-CO2-H2O mixture that can significantly influence the subsequent steps of the replacement process. In the present work, we study the evolution of dissolved gas molecules in this mixture by applying classical molecular dynamics simulations. Our study shows that a higher CO2 : N2 ratio in the mixture enhances the formation of nanobubbles composed of N2, CH4 and CO2 molecules...
March 21, 2018: Physical Chemistry Chemical Physics: PCCP
Tanai Cardona
When and how oxygenic photosynthesis originated remains controversial. Wide uncertainties exist for the earliest detection of biogenic oxygen in the geochemical record or the origin of water oxidation in ancestral lineages of the phylum Cyanobacteria. A unique trait of oxygenic photosynthesis is that the process uses a Type I reaction centre with a heterodimeric core, also known as Photosystem I, made of two distinct but homologous subunits, PsaA and PsaB. In contrast, all other known Type I reaction centres in anoxygenic phototrophs have a homodimeric core...
March 2018: Heliyon
Gabriela Basile Carballo, Jéssica Ribeiro Honorato, Giselle Pinto Farias de Lopes, Tania Cristina Leite de Sampaio E Spohr
Hedgehog (Hh) signaling pathway plays an essential role during vertebrate embryonic development and tumorigenesis. It is already known that Sonic hedgehog (Shh) pathway is important for the evolution of radio and chemo-resistance of several types of tumors. Most of the brain tumors are resistant to chemotherapeutic drugs, consequently, they have a poor prognosis. So, a better knowledge of the Shh pathway opens an opportunity for targeted therapies against brain tumors considering a multi-factorial molecular overview...
March 20, 2018: Cell Communication and Signaling: CCS
Li Bao, Zhaoyang Qian, Maria B Lyng, Ling Wang, Yuan Yu, Ting Wang, Xiuqing Zhang, Huanming Yang, Nils Brünner, Jun Wang, Henrik J Ditzel
Single cancer cell sequencing studies currently use randomly-selected cells, limiting correlations between genomic aberrations, morphology and spatial localization. We laser-captured microdissected single cells from morphologically-distinct areas of primary breast cancer and corresponding lymph node metastasis and performed whole-exome or deep-target sequencing of greater than 100 such cells. Two major subclones co-existed in different areas of the primary tumor, and the lymph node metastasis originated from a minor subclone in the invasive front of the primary tumor with additional copy number changes including 8q gain, but no additional point mutations in driver genes...
March 15, 2018: Journal of Clinical Investigation
Zewdu Hora, Solomon Zewdu Altaye, Abebe Jenberie Wubie, Jianke Li
The honeybee is one of the most valuable insect pollinators, which plays a key role in pollinating wild vegetation and agricultural crops, with significant contribution to world food production. Although honeybees have long been studied as model for social evolution, the molecular level of honeybee biology remained poorly understood until the year 2006. With the available honeybee genome sequence, technological advancements in protein separation, mass spectrometry, and bioinformatics, wide ranges of honeybee biology such as developmental biology, physiology, behavior, neurobiology, and immunology are explored to a new depth at molecular and biochemical levels...
March 20, 2018: Journal of Agricultural and Food Chemistry
Qi Wang, Qian Wang, Yan-Le Zhou, Shuang Shan, Huan-Huan Cui, Yong Xiao, Kun Dong, Adel Khashaveh, Liang Sun, Yong-Jun Zhang
The phytophagous mirid bugs of Apolygus lucorum, Lygus pratensis as well as three Adelphocoris spp., including Adelphocoris lineolatus, A. suturalis , and A. fasciaticollis are major pests of multiple agricultural crops in China, which have distinct geographical distribution and occurrence ranges. Like many insect species, these bugs heavily rely on olfactory cues to search preferred host plants, thereby investigation on functional co-evolution and divergence of olfactory genes seems to be necessary and is of great interest...
2018: Frontiers in Physiology
Tom Verbiest, Rosemary Finnon, Natalie Brown, Lourdes Cruz-Garcia, Paul Finnon, Grainne O'Brien, Eleanor Ross, Simon Bouffler, Cheryl L Scudamore, Christophe Badie
Epidemiological studies have demonstrated an increased leukemia incidence following ionizing radiation exposure, but to date, the target cells and underlying mechanisms of radiation leukemogenesis remain largely unidentified. We engineered a mouse model carrying a different fluorescent marker on each chromosome 2, located inside the minimum deleted region occurring after radiation exposure and recognized as the first leukemogenic event. Using this tailored model, we report that following radiation exposure, more than half of asymptomatic CBA Sfpi1 GFP/mCh mice presented with expanding clones of preleukemic hematopoietic cells harboring a hemizygous interstitial deletion of chromosome 2...
March 3, 2018: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
Jared A Grummer, Mariana M Morando, Luciano J Avila, Jack W Sites, Adam D Leaché
Rapid evolutionary radiations are difficult to resolve because divergence events are nearly synchronous and gene flow among nascent species can be high, resulting in a phylogenetic "bush". Large datasets composed of sequence loci from across the genome can potentially help resolve some of these difficult phylogenetic problems. A suitable test case is the Liolaemus fitzingerii species group of lizards, which includes twelve species that are broadly distributed in Argentinean Patagonia. The species in the group have had a complex evolutionary history that has led to high morphological variation and unstable taxonomy...
March 16, 2018: Molecular Phylogenetics and Evolution
Yuwei Zhu, Fan Zhang, Zhiwei Huang
A molecular arms race is progressively being unveiled between prokaryotes and viruses. Prokaryotes utilize CRISPR-mediated adaptive immune systems to kill the invading phages and mobile genetic elements, and in turn, the viruses evolve diverse anti-CRISPR proteins to fight back. The structures of several anti-CRISPR proteins have now been reported, and here we discuss their structural features, with a particular emphasis on topology, to discover their similarities and differences. We summarize the CRISPR-Cas inhibition mechanisms of these anti-CRISPR proteins in their structural context...
March 19, 2018: BMC Biology
Denis Warshan, Anton Liaimer, Eric Pederson, Sea-Yong Kim, Nicole Shapiro, Tanja Woyke, Bjørn Altermark, Katharina Pawlowski, Philip D Weyman, Christopher L Dupont, Ulla Rasmussen
The cyanobacteria belonging to the genus Nostoc comprise free-living strains but also facultative plant-symbionts. Symbiotic strains can enter into symbiosis with taxonomically diverse range of host plants. Little is known about genomic changes associated with evolutionary transition of Nostoc from free-living to plant symbiont. Here we compared the genomes derived from eleven symbiotic Nostoc strains isolated from different host plants and infer phylogenetic relationships between strains. Phylogenetic reconstructions of 89 Nostocales showed that symbiotic Nostoc strains with a broad host range, entering epiphytic and intracellular or extracellular endophytic interactions, form a monophyletic clade indicating a common evolutionary history...
March 15, 2018: Molecular Biology and Evolution
Xiao Yi
Biological functions - studied by molecular, systems and behavioral biology - are referred to as proximate mechanisms. Why and how they have emerged from the course of evolution are referred to as ultimate mechanisms. Despite the conceptual and technical schism between the disciplines that focus on each, studies from one side can benefit the other. Experimental evolution is an emerging field at the crossroads of functional and evolutionary biology. Herein microorganisms and mammalian cell lines evolve in well-controlled laboratory environments over multiple generations...
December 2017: Synthetic and Systems Biotechnology
Ava Yuan Xue, Antonella Di Pizio, Anat Levit, Tali Yarnitzky, Osnat Penn, Tal Pupko, Masha Y Niv
The 25 human bitter taste receptors (hT2Rs) recognize thousands of structurally and chemically diverse bitter substances. The binding modes of human bitter taste receptors hT2R10 and hT2R46, which are responsible for strychnine recognition, were previously established using site-directed mutagenesis, functional assays, and molecular modeling. Here we construct a phylogenetic tree and reconstruct ancestral sequences of the T2R10 and T2R46 clades. We next analyze the binding sites in view of experimental data to predict their ability to recognize strychnine...
2018: Frontiers in Molecular Biosciences
Muhammad Abdullah, Yunpeng Cao, Xi Cheng, Awais Shakoor, Xueqiang Su, Junshan Gao, Yongping Cai
The SQUAMOSA promoter binding protein (SBP)-box proteins are plant-specific transcriptional factors in plants. SBP TFs are known to play important functions in a diverse development process and also related in the process of evolutionary novelties. SBP gene family has been characterized in several plant species, but little is known about molecular evolution, functional divergence and comprehensive study of SBP gene family in Rosacea. We carried out genome-wide investigations and identified 14, 32, 17, and 17 SBP genes from four Rosacea species ( Fragaria vesca , Pyrus bretschneideri, Prunus persica and Prunus mume , respectively)...
2018: Frontiers in Genetics
Liang-Qing Dong, Yang Shi, Li-Jie Ma, Liu-Xiao Yang, Xiao-Ying Wang, Shu Zhang, Zhi-Chao Wang, Meng Duan, Zhao Zhang, Long-Zi Liu, Bo-Hao Zheng, Zhen-Bin Ding, Ai-Wu Ke, Da-Ming Gao, Ke Yuan, Jian Zhou, Jia Fan, Ruibin Xi, Qiang Gao
BACKGROUND & AIMS: Intrahepatic cholangiocarcinoma (ICC) is the second-most lethal primary liver cancer. Little is known about intratumoral heterogeneity (ITH) and its impact on ICC progression. We aim to investigate its ITH in hope of helping develop new therapeutic strategies. METHODS: We obtained 69 spatially distinct regions from 6 operable ICCs. Patient-derived primary cancer cells (PDPCs) were established for each region, followed by whole-exome sequencing(WES) and multi-level validation...
March 15, 2018: Journal of Hepatology
David Barros-García, Elsa Froufe, Rafael Bañón, Juan Carlos Arronte, Alejandro De Carlos
The Notacanthiformes is an ancient group of deep-sea ray-finned fishes comprising 27 species in two families; Halosauridae and Notacanthidae. Although many studies have tried to reconstruct the phylogenetic relationships among the major clades of Elopomorpha, little is known about the evolutionary history of notacanthiforms. Molecular and morphological data were used to test previous hypotheses regarding the phylogenetic relationships among notacanthiform taxa, and to unravel the origin and evolution of this group...
March 15, 2018: Molecular Phylogenetics and Evolution
Joshua P Egan, Devin D Bloom, Chien-Hsien Kuo, Michael P Hammer, Prasert Tongnunui, Samuel P Iglésias, Marcus Sheaves, Chaiwut Grudpan, Andrew M Simons
Biotic and abiotic forces govern the evolution of trophic niches, which profoundly impact ecological and evolutionary processes and aspects of species biology. Herbivory is a particularly interesting trophic niche because there are theorized trade-offs associated with diets comprised of low quality food that might prevent the evolution of herbivory in certain environments. Herbivory has also been identified as a potential evolutionary "dead-end" that hinders subsequent trophic diversification. For this study we investigated trophic niche evolution in Clupeoidei (anchovies, sardines, herrings, and their relatives) and tested the hypotheses that herbivory is negatively correlated with salinity and latitude using a novel, time-calibrated molecular phylogeny, trophic guilds delimited using diet data and cluster analysis, and standard and phylogenetically-informed statistical methods...
March 15, 2018: Molecular Phylogenetics and Evolution
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