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"Evolutionary mechanisms"

Steven M Whitfield, Gilbert Alvarado, Juan Abarca, Hector Zumbado, Ibrahim Zuñiga, Mark Wainwright, Jacob Kerby
Global amphibian biodiversity has declined dramatically in the past 4 decades, and many amphibian species have declined to near extinction as a result of emergence of the amphibian chytrid fungus, Batrachochytrium dendrobatidis (Bd). However, persistent or recovering populations of several amphibian species have recently been rediscovered, and such populations may illustrate how amphibian species that are highly susceptible to chytridiomycosis may survive in the presence of Bd. We conducted field surveys for Bd infection in 7 species of Costa Rican amphibians (all species that have declined to near extinction but for which isolated populations persist) to characterize infection profiles in highly Bd-susceptible amphibians post-decline...
September 20, 2017: Diseases of Aquatic Organisms
Patrícia Barbosa, Eliza Viola Leal, Maelin da Silva, Mara Cristina de Almeida, Orlando Moreira-Filho, Roberto Ferreira Artoni
DNA sequences of multiple copies help in understanding evolutionary mechanisms, genomic structures and karyotype differentiation. The current study investigates the organization and distribution of different repetitive DNA in the standard complement and B chromosomes in Astyanax scabripinnis (Jenyns, 1842) chromosomes from three allopatric populations in Campos do Jordão region, São Paulo State, Brazil. The location of microsatellite sequences showed different chromosome distribution between Lavrinha Farm Stream (LFS) and Lake of Pedalinho (LP) populations...
2017: Comparative Cytogenetics
Ick-Hyun Jo, Jinsu Lee, Chi Eun Hong, Dong Jin Lee, Wonsil Bae, Sin-Gi Park, Yong Ju Ahn, Young Chang Kim, Jang Uk Kim, Jung Woo Lee, Dong Yun Hyun, Sung-Keun Rhee, Chang Pyo Hong, Kyong Hwan Bang, Hojin Ryu
Korean ginseng (Panax ginseng C.A. Meyer) has been widely used for medicinal purposes and contains potent plant secondary metabolites, including ginsenosides. To obtain transcriptomic data that offers a more comprehensive view of functional genomics in P. ginseng, we generated genome-wide transcriptome data from four different P. ginseng tissues using PacBio isoform sequencing (Iso-Seq) technology. A total of 135,317 assembled transcripts were generated with an average length of 3.2 kb and high assembly completeness...
September 15, 2017: Genes
Carol Zastavniouk, Laura K Weir, Dylan J Fraser
A reduction in population size due to habitat fragmentation can alter the relative roles of different evolutionary mechanisms in phenotypic trait differentiation. While deterministic (selection) and stochastic (genetic drift) mechanisms are expected to affect trait evolution, genetic drift may be more important than selection in small populations. We examined relationships between mature adult traits and ecological (abiotic and biotic) variables among 14 populations of brook trout. These naturally fragmented populations have shared ancestry but currently exhibit considerable variability in habitat characteristics and population size (49 < Nc < 10,032; 3 < Nb < 567)...
September 2017: Ecology and Evolution
Mohammed Ba Abdullah, Richard Palermo, Anne Palser, Nicholas E Grayson, Paul Kellam, Samantha Correia, Agnieszka Szymula, Rob White
Epstein-Barr virus (EBV) is a ubiquitous pathogen of humans that can cause several types of lymphoma and carcinoma. Like other herpesviruses, EBV has diversified both through co-evolution with its host, and genetic exchange between virus strains. Sequence analysis of the EBV genome is unusually challenging, because of the large number and length of repeat regions within the virus. Here we describe the sequence assembly and analysis of the large internal repeat of EBV (IR1 or BamW repeats) from over 70 strains...
September 13, 2017: Journal of Virology
Dario Leister
The term 'experimental evolution' refers to short-term evolutionary experiments with microorganisms under controlled conditions in which selection is expected to occur. In combination with whole-genome sequencing and genetic engineering, the method has become a powerful tool to study evolutionary mechanisms and engineer new microbial variants. It has been most extensively used in the model species Escherichia coli and Saccharomyces cerevisiae, but more recently photosynthetic microorganisms have been subjected to experimental evolution...
September 7, 2017: Essays in Biochemistry
Lei Huang, Li Liao, Cathy H Wu
Prediction of protein-protein interaction (PPI) remains a central task in systems biology. With more PPIs identified, forming PPI networks, it has become feasible and also imperative to study PPIs at the network level, such as evolutionary analysis of the networks, for better understanding of PPI networks and for more accurate prediction of pairwise PPIs by leveraging the information gained at the network level. In this work we developed a novel method that enables us to incorporate evolutionary information into geometric space to improve PPI prediction, which in turn can be used to select and evaluate various evolutionary models...
2017: PloS One
Cesc Múrria, Núria Bonada, Mark Vellend, Carmen Zamora-Muñoz, Javier Alba-Tercedor, Carmen Elisa Sainz-Cantero, Josefina Garrido, Raul Acosta, Majida El Alami, Jose Barquín, Tomáš Derka, Mario Álvarez-Cabria, Marta Sáinz-Bariain, Ana F Filipe, Alfried P Vogler
Community assembly is determined by a combination of historical events and contemporary processes that are difficult to disentangle, but eco-evolutionary mechanisms may be uncovered by the joint analysis of species and genetic diversity across multiple sites. Mountain streams across Europe harbour highly diverse macroinvertebrate communities whose composition and turnover (replacement of taxa) among sites and regions remain poorly known. We studied whole-community biodiversity within and among six mountain regions along a latitudinal transect from Morocco to Scandinavia at three levels of taxonomic hierarchy: genus, species and haplotypes...
September 7, 2017: Molecular Ecology
Hamed S Najafabadi, Michael Garton, Matthew T Weirauch, Sanie Mnaimneh, Ally Yang, Philip M Kim, Timothy R Hughes
BACKGROUND: The C2H2 zinc finger (C2H2-ZF) is the most numerous protein domain in many metazoans, but is not as frequent or diverse in other eukaryotes. The biochemical and evolutionary mechanisms that underlie the diversity of this DNA-binding domain exclusively in metazoans are, however, mostly unknown. RESULTS: Here, we show that the C2H2-ZF expansion in metazoans is facilitated by contribution of non-base-contacting residues to DNA binding energy, allowing base-contacting specificity residues to mutate without catastrophic loss of DNA binding...
September 6, 2017: Genome Biology
Chao Du, Lifang Zhang, Ting Lu, Jingnan Ma, Chenjuan Zeng, Bisong Yue, Xiuyue Zhang
BACKGROUND: Insect mitochondrial genomes (mitogenomes) exhibit high diversity in some lineages. The gene rearrangement and large intergenic spacer (IGS) have been reported in several Coleopteran species, although very little is known about mitogenomes of Meloidae. RESULTS: We determined complete or nearly complete mitogenomes of seven meloid species. The circular genomes encode 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs) and two ribosomal RNAs (rRNAs), and contain a control region, with gene arrangement identical to the ancestral type for insects...
September 6, 2017: BMC Genomics
Daniel M Quinn, Joseph Topczewski, Nilanthi Yasapala, Alexander Lodge
Organophosphorus agents are potent inhibitors of acetylcholinesterase. Inhibition involves successive chemical events. The first is phosphylation of the active site serine to produce a neutral adduct, which is a close structural analog of the acylation transition state. This adduct is unreactive toward spontaneous hydrolysis, but in many cases can be reactivated by nucleophilic medicinal agents, such as oximes. However, the initial phosphylation reaction may be followed by a dealkylation reaction of the incipient adduct...
September 4, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Luis M San-Jose, Valérie Ducret, Anne-Lyse Ducrest, Céline Simon, Alexandre Roulin
The mean phenotypic effects of a discovered variant help to predict major aspects of the evolution and inheritance of a phenotype. However, differences in the phenotypic variance associated to distinct genotypes are often overlooked despite being suggestive of processes that largely influence phenotypic evolution, such as interactions between the genotypes with the environment or the genetic background. We present empirical evidence for a mutation at the melanocortin-1-receptor gene, a major vertebrate coloration gene, affecting phenotypic variance in the barn owl, Tyto alba...
September 1, 2017: Evolution; International Journal of Organic Evolution
Anderson F Brito, John W Pinney
To study virus-host protein interactions, knowledge about viral and host protein architectures and repertoires, their particular evolutionary mechanisms, and information on relevant sources of biological data is essential. The purpose of this review article is to provide a thorough overview about these aspects. Protein domains are basic units defining protein interactions, and the uniqueness of viral domain repertoires, their mode of evolution, and their roles during viral infection make viruses interesting models of study...
2017: Frontiers in Microbiology
Anja Kögler, Thomas Schmidt, Torsten Wenke
Short interspersed nuclear elements (SINEs) are non-autonomous transposable elements which are propagated by retrotransposition and constitute an inherent part of the genome of most eukaryotic species. Knowledge of heterogeneous and highly abundant SINEs is crucial for the de novo or improvement of annotation of whole genome sequences. We scanned Poaceae genome sequences of six important cereals (Oryza sativa, Triticum aestivum, Hordeum vulgare, Panicum virgatum, Sorghum bicolor, Zea mays) and Brachypodium distachyon to examine the diversity and evolution of SINE populations...
August 30, 2017: Plant Journal: for Cell and Molecular Biology
Keisha D Carlson, Noe Fernandez-Pozo, Aureliano Bombarely, Rahul Pisupati, Lukas A Mueller, Andreas Madlung
BACKGROUND: Allopolyploids contain genomes composed of more than two complete sets of chromosomes that originate from at least two species. Allopolyploidy has been suggested as an important evolutionary mechanism that can lead to instant speciation. Arabidopsis suecica is a relatively recent allopolyploid species, suggesting that its natural accessions might be genetically very similar to each other. Nonetheless, subtle phenotypic differences have been described between different geographic accessions of A...
August 23, 2017: BMC Genomics
Saradee Sengupta, Martín D Ezcurra, Saswati Bandyopadhyay
The early evolution of archosauromorphs (bird- and crocodile-line archosaurs and stem-archosaurs) represents an important case of adaptive radiation that occurred in the aftermath of the Permo-Triassic mass extinction. Here we enrich the early archosauromorph record with the description of a moderately large (3-4 m in total length), herbivorous new allokotosaurian, Shringasaurus indicus, from the early Middle Triassic of India. The most striking feature of Shringasaurus indicus is the presence of a pair of large supraorbital horns that resemble those of some ceratopsid dinosaurs...
August 21, 2017: Scientific Reports
Alisa O Vershinina, Vladimir A Lukhtanov
Despite predictions of the classic, hybrid-sterility model of chromosomal speciation, some organisms demonstrate high rate of karyotype evolution. This rate is especially impressive in Agrodiaetus butterflies that rapidly evolved the greatest chromosome number diversity known in animal kingdom within a single subgenus. Here we analyzed karyotype evolution in Agrodiaetus using phylogenetic comparative methods. We found that chromosome numbers possess a strong phylogenetic signal. This disproves the chromosome megaevolution model that proposes multiple chromosome rearrangements to accumulate independently in each of closely related species...
August 15, 2017: Scientific Reports
Lucas D Gorné, Sandra Díaz
A classic topic in ecology and evolution, phenotypic microevolution of quantitative traits has received renewed attention in the face of rapid global environmental change. However, for plants, synthesis has been hampered by the limited use of standard metrics, which makes it difficult to systematize empirical information. Here we demonstrate the advantages of incorporating meta-analysis tools to the review of microevolutionary rates. We perform a systematic survey of the plant literature on microevolution of quantitative traits over known periods of time, based on the scopus database...
August 2017: Ecology and Evolution
Lotte A van Boheemen, Eric Lombaert, Kristin A Nurkowski, Bertrand Gauffre, Loren H Rieseberg, Kathryn A Hodgins
Admixture between differentiated populations is considered to be a powerful mechanism stimulating the invasive success of some introduced species. It is generally facilitated through multiple introductions; however, the importance of admixture prior to introduction has rarely been considered. We assess the likelihood that the invasive Ambrosia artemisiifolia populations of Europe and Australia developed through multiple introductions or were sourced from a historical admixture zone within native North America...
August 12, 2017: Molecular Ecology
Yun-Peng Du, Yu Bi, Ming-Fang Zhang, Feng-Ping Yang, Gui-Xia Jia, Xiu-Hai Zhang
Genome size (GS) diversity is of fundamental biological importance. The occurrence of giant genomes in angiosperms is restricted to just a few lineages in the analyzed genome size of plant species so far. It is still an open question whether GS diversity is shaped by neutral or natural selection. The genus Lilium, with giant genomes, is phylogenetically and horticulturally important and is distributed throughout the northern hemisphere. GS diversity in Lilium and the underlying evolutionary mechanisms are poorly understood...
2017: Frontiers in Plant Science
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