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Evolutionary biology

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https://www.readbyqxmd.com/read/28431105/extinction-vs-rapid-radiation-the-juxtaposed-evolutionary-histories-of-coelotine-spiders-support-the-eocene-oligocene-orogenesis-of-the-tibetan-plateau
#1
Zhe Zhao, Shuqiang Li
Evolutionary biology has long been concerned with how changing environments affect and drive the spatiotemporal development of organisms. Coelotine spiders (Agelenidae: Coelotinae) are common species in the temperate and subtropical areas of the Northern Hemisphere. Their long evolutionary history and the extremely imbalanced distribution of species richness suggest that Eurasian environments, especially since the Cenozoic, are the drivers of their diversification. We use phylogenetics, molecular dating, ancestral area reconstructions, diversity, and ecological niche analyses to investigate the spatiotemporal evolution of 286 coelotine species from throughout the region...
April 20, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28429314/evolutionary-origin-of-euglena
#2
Bożena Zakryś, Rafał Milanowski, Anna Karnkowska
Euglenids (Excavata, Discoba, Euglenozoa, Euglenida) is a group of free-living, single-celled flagellates living in the aquatic environments. The uniting and unique morphological feature of euglenids is the presence of a cell covering called the pellicle. The morphology and organization of the pellicle correlate well with the mode of nutrition and cell movement. Euglenids exhibit diverse modes of nutrition, including phagotrophy and photosynthesis. Photosynthetic species (Euglenophyceae) constitute a single subclade within euglenids...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28428870/gene-expression-profiling-during-the-embryo-to-larva-transition-in-the-giant-red-sea-urchin-mesocentrotus-franciscanus
#3
Juan Diego Gaitán-Espitia, Gretchen E Hofmann
In echinoderms, major morphological transitions during early development are attributed to different genetic interactions and changes in global expression patterns that shape the regulatory program for the specification of embryonic territories. In order more thoroughly to understand these biological and molecular processes, we examined the transcriptome structure and expression profiles during the embryo-to-larva transition of a keystone species, the giant red sea urchin Mesocentrotus franciscanus. Using a de novo assembly approach, we obtained 176,885 transcripts from which 60,439 (34%) had significant alignments to known proteins...
April 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28428847/lichen-acclimation-to-changing-environments-photobiont-switching-vs-climate-specific-uniqueness-in-psora-decipiens
#4
Laura Williams, Claudia Colesie, Anna Ullmann, Martin Westberg, Mats Wedin, Burkhard Büdel
Unraveling the complex relationship between lichen fungal and algal partners has been crucial in understanding lichen dispersal capacity, evolutionary processes, and responses in the face of environmental change. However, lichen symbiosis remains enigmatic, including the ability of a single fungal partner to associate with various algal partners. Psora decipiens is a characteristic lichen of biological soil crusts (BSCs), across semi-arid, temperate, and alpine biomes, which are particularly susceptible to habitat loss and climate change...
April 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28428077/molecular-bases-of-the-crosstalk-between-bone-and-muscle
#5
Gerard Karsenty, Paula Mera
Exercise is an evolutionary conserved survival function that nowadays has beneficial health effects. The increased metabolic activity of contracting skeletal muscle affects the biology of many organs involved in regulating muscle functions. The discovery of hormones and cytokines secreted by bone and skeletal muscle during exercise, has recently added experimental credence to the notion that a crosstalk exists between these organs. Bone through the hormone osteocalcin, promotes exercise capacity in the mouse...
April 17, 2017: Bone
https://www.readbyqxmd.com/read/28427327/analysis-of-transcriptome-data-reveals-multifactor-constraint-on-codon-usage-in-taenia-multiceps
#6
Xing Huang, Jing Xu, Lin Chen, Yu Wang, Xiaobin Gu, Xuerong Peng, Guangyou Yang
BACKGROUND: Codon usage bias (CUB) is an important evolutionary feature in genomes that has been widely observed in many organisms. However, the synonymous codon usage pattern in the genome of T. multiceps remains to be clarified. In this study, we analyzed the codon usage of T. multiceps based on the transcriptome data to reveal the constraint factors and to gain an improved understanding of the mechanisms that shape synonymous CUB. RESULTS: Analysis of a total of 8,620 annotated mRNA sequences from T...
April 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28424728/landscape-population-genomics-of-forsythia-forsythia-suspensa-reveal-that-ecological-habitats-determine-the-adaptive-evolution-of-species
#7
Jie Yang, Cai-Yun Miao, Run-Li Mao, Yong Li
Understanding the genetic mechanisms of adaptation to environmental variables is a key concern in molecular ecology and evolutionary biology. Determining the adaptive evolutionary direction and evaluating the adaptation status of species can improve our understanding of these mechanisms. In this study, we sampled 20 populations of Forsythia suspensa to infer the relationship between environmental variables and adaptive genetic variations. Population structure analysis revealed that four genetic groups of F...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28424494/predictable-phenotypic-but-not-karyotypic-evolution-of-populations-with-contrasting-initial-history
#8
Pedro Simões, Inês Fragata, Sofia G Seabra, Gonçalo S Faria, Marta A Santos, Michael R Rose, Mauro Santos, Margarida Matos
The relative impact of selection, chance and history will determine the predictability of evolution. There is a lack of empirical research on this subject, particularly in sexual organisms. Here we use experimental evolution to test the predictability of evolution. We analyse the real-time evolution of Drosophila subobscura populations derived from contrasting European latitudes placed in a novel laboratory environment. Each natural population was sampled twice within a three-year interval. We study evolutionary responses at both phenotypic (life-history, morphological and physiological traits) and karyotypic levels for around 30 generations of laboratory culture...
April 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28423569/accurate-prediction-of-protein-protein-interactions-by-integrating-potential-evolutionary-information-embedded-in-pssm-profile-and-discriminative-vector-machine-classifier
#9
Zheng-Wei Li, Zhu-Hong You, Xing Chen, Li-Ping Li, De-Shuang Huang, Gui-Ying Yan, Ru Nie, Yu-An Huang
Identification of protein-protein interactions (PPIs) is of critical importance for deciphering the underlying mechanisms of almost all biological processes of cell and providing great insight into the study of human disease. Although much effort has been devoted to identifying PPIs from various organisms, existing high-throughput biological techniques are time-consuming, expensive, and have high false positive and negative results. Thus it is highly urgent to develop in silico methods to predict PPIs efficiently and accurately in this post genomic era...
April 4, 2017: Oncotarget
https://www.readbyqxmd.com/read/28423081/long-wavelength-sensitive-opsin-lws-gene-variability-in-neotropical-cichlids-teleostei-cichlidae
#10
Thomaz M C Fabrin, Sonia Maria A P Prioli, Alberto José Prioli
Cichlid fishes are an important group in evolutionary biology due to their fast speciation. This group depends widely of vision for feeding and reproduction. During the evolutionary process it plays a significant role in interspecific and intraspecific recognition and in its ecology. The molecular basis of vision is formed by the interaction of the protein opsin and retinal chromophore. Long-wavelength sensitive opsin (LWS) gene is the most variable among the opsin genes and it has an ecological significance...
January 2017: Anais da Academia Brasileira de Ciências
https://www.readbyqxmd.com/read/28422426/dinosaurs-chameleons-humans-and-evo-devo-path-linking-%C3%A3-tienne-geoffroy-s-teratology-waddington-s-homeorhesis-alberch-s-logic-of-monsters-and-goldschmidt-hopeful-monsters
#11
REVIEW
Rui Diogo, Geoffrey Guinard, Raul E Diaz
Since the rise of evo-devo (evolutionary developmental biology) in the 1980s, few authors have attempted to combine the increasing knowledge obtained from the study of model organisms and human medicine with data from comparative anatomy and evolutionary biology in order to investigate the links between development, pathology, and macroevolution. Fortunately, this situation is slowly changing, with a renewed interest in evolutionary developmental pathology (evo-devo-path) in the past decades, as evidenced by the idea to publish this special, and very timely, issue on "Developmental Evolution in Biomedical Research...
May 2017: Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution
https://www.readbyqxmd.com/read/28422135/genomic-evidence-of-hybridization-between-two-independent-invasions-of-european-green-crab-carcinus-maenas-in-the-northwest-atlantic
#12
N W Jeffery, C DiBacco, B F Wringe, R R E Stanley, L C Hamilton, P N Ravindran, I R Bradbury
Invasive species have been associated with significant negative impacts in their introduced range often outcompeting native species, yet the long-term evolutionary dynamics of biological invasions are not well understood. Hybridization, either among waves of invasion or between native and introduced populations, could alter the ecological and evolutionary impacts of invasions yet has rarely been studied in marine invasive species. The European green crab (Carcinus maenas) invaded eastern North America twice from northern and southern locations in its native range...
April 19, 2017: Heredity
https://www.readbyqxmd.com/read/28422050/k-mer-content-correlation-and-position-analysis-of-genome-dna-sequences-for-the-identification-of-function-and-evolutionary-features
#13
Aaron Sievers, Katharina Bosiek, Marc Bisch, Chris Dreessen, Jascha Riedel, Patrick Froß, Michael Hausmann, Georg Hildenbrand
In genome analysis, k-mer-based comparison methods have become standard tools. However, even though they are able to deliver reliable results, other algorithms seem to work better in some cases. To improve k-mer-based DNA sequence analysis and comparison, we successfully checked whether adding positional resolution is beneficial for finding and/or comparing interesting organizational structures. A simple but efficient algorithm for extracting and saving local k-mer spectra (frequency distribution of k-mers) was developed and used...
April 19, 2017: Genes
https://www.readbyqxmd.com/read/28421292/phylogenetic-insight-into-zika-and-emerging-viruses-for-a-perspective-on-potential-hosts
#14
Diana S Weber, Karen A Alroy, Samuel M Scheiner
Global viral diversity is substantial, but viruses that contribute little to the public health burden or to agricultural damage receive minimal attention until a seemingly unimportant virus becomes a threat. The Zika virus (ZIKV) illustrated this, as there was limited information and awareness of the virus when it was identified as a public health emergency in February 2016. Predicting which virus may pose a future threat is difficult. This is in part because significant knowledge gaps in the basic biology and ecology of an emerging virus can impede policy development, delay decision making, and hinder public health action...
April 18, 2017: EcoHealth
https://www.readbyqxmd.com/read/28419279/primates-lice-and-bacteria-speciation-and-genome-evolution-in-the-symbionts-of-hominid-lice
#15
Bret M Boyd, Julie M Allen, Nam-Phuong Nguyen, Pranjal Vachaspati, Zach Quicksall, Tandy Warnow, Lawrence Mugisha, Kevin P Johnson, David L Reed
Insects with restricted diets rely on symbiotic bacteria to provide essential metabolites missing in their diet. The blood-sucking lice are obligate, host-specific parasites of mammals and are themselves host to symbiotic bacteria. In human lice, these bacterial symbionts supply the lice with B-vitamins. Here we sequenced the genomes of symbiotic and heritable bacterial of human, chimpanzee, gorilla, and monkey lice and used phylogenomics to investigate their evolutionary relationships. We find that these symbionts have a phylogenetic history reflecting the louse phylogeny, a finding contrary to previous reports of symbiont replacement...
April 14, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28419089/erroneous-energy-generating-cycles-in-published-genome-scale-metabolic-networks-identification-and-removal
#16
Claus Jonathan Fritzemeier, Daniel Hartleb, Balázs Szappanos, Balázs Papp, Martin J Lercher
Energy metabolism is central to cellular biology. Thus, genome-scale models of heterotrophic unicellular species must account appropriately for the utilization of external nutrients to synthesize energy metabolites such as ATP. However, metabolic models designed for flux-balance analysis (FBA) may contain thermodynamically impossible energy-generating cycles: without nutrient consumption, these models are still capable of charging energy metabolites (such as ADP→ATP or NADP+→NADPH). Here, we show that energy-generating cycles occur in over 85% of metabolic models without extensive manual curation, such as those contained in the ModelSEED and MetaNetX databases; in contrast, such cycles are rare in the manually curated models of the BiGG database...
April 18, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28414521/representations-of-search-spaces-in-the-problem-of-mutational-pressure-optimization-according-to-protein-coding-sequences
#17
Paweł Błażej, Małgorzata Wnętrzak, Małgorzata Grabińska, Paweł Mackiewicz
The proper representation of the search space is the fundamental step in every optimization task, because it has a decisive impact on the quality of potential solutions. In particular, this problem appears when the search spaces are nonstandard and complex, with the large number of candidate solutions that differ from classical forms usually investigated. One of such spaces is the set of continuous-time, homogenous, and stationary Markov processes. They are commonly used to describe biological phenomena, for example, mutations in DNA sequences and their evolution...
April 17, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28413063/amniotic-membrane-application-for-the-healing-of-chronic-wounds-and-ulcers
#18
Gregorio Castellanos, Ángel Bernabé-García, José M Moraleda, Francisco J Nicolás
Wound healing usually follows a predictable sequence and prognosis of events. Its evolutionary process is the result of a complicated interaction between patient-related factors, the wound, the treatment used and the skills and knowledge of the professionals who treat them. Only through a meticulous initial assessment of the wound is it possible to identify the factors that contribute to its complexity. The challenge for professionals will be to implement efficient therapies at the right time and in the most cost-efficient way in order to reduce associated problems, treat the symptoms and expectations of the patients and achieve adequate wound healing whenever possible...
April 10, 2017: Placenta
https://www.readbyqxmd.com/read/28412903/phage-life-cycles-behind-bacterial-biodiversity
#19
Tomasz Olszak, Agnieszka Latka, Bartosz Roszniowski, Miguel Angel Valvano, Zuzanna Drulis-Kawa
Bacteriophages (phages or bacterial viruses) are the most abundant biological entities in our planet; their influence reaches far beyond the microorganisms they parasitize. Phages are present in every environment and shape up every bacterial population in both active and passive ways. They participate in the circulation of organic matter and drive the evolution of microorganisms by horizontal gene transfer at unprecedented scales. The mass flow of genetic information in the microbial world influences the biosphere and poses challenges for science and medicine...
April 13, 2017: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/28411839/the-molecular-revolution-in-cutaneous-biology-edc-and-locus-control
#20
REVIEW
Inez Y Oh, Cristina de Guzman Strong
The epidermal differentiation complex (EDC) locus consists of a cluster of genes important for the terminal differentiation of the epidermis. While early studies identified the functional importance of individual EDC genes, the recognition of the EDC genes as a cluster with its shared biology, homology, and physical linkage was pivotal to later studies that investigated the transcriptional regulation of the locus. Evolutionary conservation of the EDC and the transcriptional activation during epidermal differentiation suggested a cis-regulatory mechanism via conserved noncoding elements or enhancers...
May 2017: Journal of Investigative Dermatology
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