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"Evolutionary history"

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https://www.readbyqxmd.com/read/29153402/phylogenetics-and-phylogenomics-of-rust-fungi
#1
M Catherine Aime, Alistair R McTaggart, Stephen J Mondo, Sébastien Duplessis
Rust fungi (Pucciniales) are the most speciose and the most complex group of plant pathogens. Historically, rust taxonomy was largely influenced by host and phenotypic characters, which are potentially plastic. Molecular systematic studies suggest that the extant diversity of this group was largely shaped by host jumps and subsequent shifts. However, it has been challenging to reconstruct the evolutionary history for the order, especially at deeper (family-level) nodes. Phylogenomics offer a potentially powerful tool to reconstruct the Pucciniales tree of life, although researchers working at this vanguard still face unprecedented challenges working with nonculturable organisms that possess some of the largest and most repetitive genomes now known in kingdom fungi...
2017: Advances in Genetics
https://www.readbyqxmd.com/read/29153401/multiple-approaches-to-phylogenomic-reconstruction-of-the-fungal-kingdom
#2
Charley G P McCarthy, David A Fitzpatrick
Fungi are possibly the most diverse eukaryotic kingdom, with over a million member species and an evolutionary history dating back a billion years. Fungi have been at the forefront of eukaryotic genomics, and owing to initiatives like the 1000 Fungal Genomes Project the amount of fungal genomic data has increased considerably over the last 5 years, enabling large-scale comparative genomics of species across the kingdom. In this chapter, we first review fungal evolution and the history of fungal genomics. We then review in detail seven phylogenomic methods and reconstruct the phylogeny of 84 fungal species from 8 phyla using each method...
2017: Advances in Genetics
https://www.readbyqxmd.com/read/29153325/genetic-and-epigenetic-strategies-potentiate-gal4-activation-to-enhance-fitness-in-recently-diverged-yeast-species
#3
Varun Sood, Jason H Brickner
Certain genes show more rapid reactivation for several generations following repression, a conserved phenomenon called epigenetic transcriptional memory. Following previous growth in galactose, GAL gene transcriptional memory confers a strong fitness benefit in Saccharomyces cerevisiae adapting to growth in galactose for up to 8 generations. A genetic screen for mutants defective for GAL gene memory revealed new insights into the molecular mechanism, adaptive consequences, and evolutionary history of memory...
November 9, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/29152711/the-burst-phase-folding-intermediate-of-ribonuclease-h-changes-conformation-over-evolutionary-history
#4
Shion A Lim, Susan Marqusee
The amino acid sequence encodes the energy landscape of a protein. Therefore, we expect evolutionary mutations to change features of the protein energy landscape, including the conformations adopted by a polypeptide as it folds to its native state. Ribonucleases H (RNase H) from Escherichia coli and Thermus thermophilus both fold via a partially folded intermediate in which the core region of the protein (helices A-D and strands 4-5) is structured. Strand 1, however, uniquely contributes to the T. thermophilus RNase H folding intermediate (Icore+1 ), but not the E...
November 20, 2017: Biopolymers
https://www.readbyqxmd.com/read/29151874/incorporating-evolutionary-insights-to-improve-ecotoxicology-for-freshwater-species
#5
Steven P Brady, Jonathan L Richardson, Bethany K Kunz
Ecotoxicological studies have provided extensive insights into the lethal and sublethal effects of environmental contaminants. These insights are critical for environmental regulatory frameworks, which rely on knowledge of toxicity for developing policies to manage contaminants. While varied approaches have been applied to ecotoxicological questions, perspectives related to the evolutionary history of focal species or populations have received little consideration. Here, we evaluate chloride toxicity from the perspectives of both macroevolution and contemporary evolution...
September 2017: Evolutionary Applications
https://www.readbyqxmd.com/read/29151866/amphibian-species-traits-evolutionary-history-and-environment-predict-batrachochytrium-dendrobatidis-infection-patterns-but-not-extinction-risk
#6
Dan A Greenberg, Wendy J Palen, Arne Ø Mooers
The fungal pathogen Batrachochytrium dendrobatidis (B. dendrobatidis) has emerged as a major agent of amphibian extinction, requiring conservation intervention for many susceptible species. Identifying susceptible species is challenging, but many aspects of species biology are predicted to influence the evolution of host resistance, tolerance, or avoidance strategies towards disease. In turn, we may expect species exhibiting these distinct strategies to differ in their ability to survive epizootic disease outbreaks...
December 2017: Evolutionary Applications
https://www.readbyqxmd.com/read/29149087/taxonomic-classification-for-living-organisms-using-convolutional-neural-networks
#7
Saed Khawaldeh, Usama Pervaiz, Mohammed Elsharnoby, Alaa Eddin Alchalabi, Nayel Al-Zubi
Taxonomic classification has a wide-range of applications such as finding out more about evolutionary history. Compared to the estimated number of organisms that nature harbors, humanity does not have a thorough comprehension of to which specific classes they belong. The classification of living organisms can be done in many machine learning techniques. However, in this study, this is performed using convolutional neural networks. Moreover, a DNA encoding technique is incorporated in the algorithm to increase performance and avoid misclassifications...
November 17, 2017: Genes
https://www.readbyqxmd.com/read/29148397/evolutionary-context-of-non-sorbitol-fermenting-shiga-toxin-producing-escherichia-coli-o55-h7
#8
Kyle Schutz, Lauren A Cowley, Sharif Shaaban, Anne Carroll, Eleanor McNamara, David L Gally, Gauri Godbole, Claire Jenkins, Timothy J Dallman
In July 2014, an outbreak of Shiga toxin-producing Escherichia coli (STEC) O55:H7 in England involved 31 patients, 13 (42%) of whom had hemolytic uremic syndrome. Isolates were sequenced, and the sequences were compared with publicly available sequences of E. coli O55:H7 and O157:H7. A core-genome phylogeny of the evolutionary history of the STEC O55:H7 outbreak strain revealed that the most parsimonious model was a progenitor enteropathogenic O55:H7 sorbitol-fermenting strain, lysogenized by a Shiga toxin (Stx) 2a-encoding phage, followed by loss of the ability to ferment sorbitol because of a non-sense mutation in srlA...
December 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/29144443/a-genomic-survey-of-scpp-family-genes-in-fishes-provides-novel-insights-into-the-evolution-of-fish-scales
#9
Yunyun Lv, Kazuhiko Kawasaki, Jia Li, Yanping Li, Chao Bian, Yu Huang, Xinxin You, Qiong Shi
The family of secretory calcium-binding phosphoproteins (SCPPs) have been considered vital to skeletal tissue mineralization. However, most previous SCPP studies focused on phylogenetically distant animals but not on those closely related species. Here we provide novel insights into the coevolution of SCPP genes and fish scales in 10 species from Otophysi. According to their scale phenotypes, these fishes can be divided into three groups, i.e., scaled, sparsely scaled, and scaleless. We identified homologous SCPP genes in the genomes of these species and revealed an absence of some SCPP members in some genomes, suggesting an uneven evolutionary history of SCPP genes in fishes...
November 16, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29141015/nematocytes-discovery-and-characterization-of-a-novel-anculeate-hemocyte-in-drosophila-falleni-and-drosophila-phalerata
#10
Julianna Bozler, Balint Z Kacsoh, Giovanni Bosco
Immune challenges, such as parasitism, can be so pervasive and deleterious that they constitute an existential threat to a species' survival. In response to these ecological pressures, organisms have developed a wide array of novel behavioral, cellular, and molecular adaptations. Research into these immune defenses in model systems has resulted in a revolutionary understanding of evolution and functional biology. As the field has expanded beyond the limited number of model organisms our appreciation of evolutionary innovation and unique biology has widened as well...
2017: PloS One
https://www.readbyqxmd.com/read/29140577/herbivory-and-drought-generate-short-term-stochasticity-and-long-term-stability-in-a-savanna-understory-community
#11
Corinna Riginos, Lauren M Porensky, Kari E Veblen, Truman P Young
Rainfall and herbivory are fundamental drivers of grassland plant dynamics, yet few studies have examined long-term interactions between these factors in an experimental setting. Understanding such interactions is important, as rainfall is becoming increasingly erratic and native wild herbivores are being replaced by livestock. Livestock grazing and episodic low rainfall are thought to interact, leading to greater community change than either factor alone. We examined patterns of change and stability in herbaceous community composition through four dry periods, or droughts, over 15 years of the Kenya Long-term Exclosure Experiment (KLEE), which consists of six different combinations of cattle, native wild herbivores (e...
November 15, 2017: Ecological Applications: a Publication of the Ecological Society of America
https://www.readbyqxmd.com/read/29138301/genomic-variation-and-evolution-of-vibrio-parahaemolyticus-st36-over-the-course-of-a-transcontinental-epidemic-expansion
#12
Jaime Martinez-Urtaza, Ronny van Aerle, Michel Abanto, Julie Haendiges, Robert A Myers, Joaquin Trinanes, Craig Baker-Austin, Narjol Gonzalez-Escalona
Vibrio parahaemolyticus is the leading cause of seafood-related infections with illnesses undergoing a geographic expansion. In this process of expansion, the most fundamental change has been the transition from infections caused by local strains to the surge of pandemic clonal types. Pandemic clone sequence type 3 (ST3) was the only example of transcontinental spreading until 2012, when ST36 was detected outside the region where it is endemic in the U.S. Pacific Northwest causing infections along the U.S. northeast coast and Spain...
November 14, 2017: MBio
https://www.readbyqxmd.com/read/29138255/complex-history-and-differentiation-patterns-of-the-t-haplotype-a-mouse-meiotic-driver
#13
Reka K Kelemen, Beatriz Vicoso
The t-haplotype, a mouse meiotic driver found on chromosome 17, has been a model for autosomal segregation distortion for close to a century, but several questions remain regarding its biology and evolutionary history. A recently published set of population genomics resources for wild mice includes several individuals heterozygous for the t-haplotype, which we use to characterize this selfish element at the genomic and transcriptomic level. Our results show that large sections of the t-haplotype have been replaced by standard homologous sequences, possibly due to occasional events of recombination, and that this complicates the inference of its history...
November 14, 2017: Genetics
https://www.readbyqxmd.com/read/29134729/maintaining-their-genetic-distance-little-evidence-for-introgression-between-widely-hybridising-species-of-geum-with-contrasting-mating-systems
#14
Crispin Y Jordan, Konrad Lohse, Frances Turner, Marian Thomson, Karim Gharbi, Richard A Ennos
Within the plant kingdom many genera contain sister lineages with contrasting outcrossing and inbreeding mating systems that are known to hybridise. The evolutionary fate of these sister lineages is likely to be influenced by the extent to which they exchange genes. We measured gene flow between outcrossing Geum rivale and selfing G. urbanum, sister species that hybridise in contemporary populations. We generated and used a draft genome of G. urbanum to develop dd-RAD data scorable in both species. Coalescent analysis of RAD data from allopatric populations indicated that the species diverged 2-3 Mya, and that historical gene flow between them was extremely low (1 migrant every 25 generations)...
November 13, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29134726/the-divergence-history-of-the-perennial-plant-linaria-cavanillesii-confirms-a-recent-loss-of-self-incompatibility
#15
Marie Voillemot, Quentin Rougemont, Camille Roux, John R Pannell
Many angiosperms prevent inbreeding through a self-incompatibility (SI) system, but the loss of SI has been frequent in their evolutionary history. The loss of SI may often lead to an increase in the selfing rate, with the purging of inbreeding depression and the ultimate evolution of a selfing syndrome, where plants have smaller flowers with reduced pollen and nectar production. In this study, we used approximate Bayesian computation (ABC) to estimate the timing of divergence between populations of the plant Linaria cavanillesii, whose populations differ in SI status and in which SI is associated with low inbreeding depression but not with a transition to full selfing or a selfing syndrome...
November 13, 2017: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/29134072/genetic-signature-of-last-glacial-maximum-regional-refugia-in-a-circum-antarctic-sea-spider
#16
Anna Soler-Membrives, Katrin Linse, Karen J Miller, Claudia P Arango
The evolutionary history of Antarctic organisms is becoming increasingly important to understand and manage population trajectories under rapid environmental change. The Antarctic sea spider Nymphon australe, with an apparently large population size compared with other sea spider species, is an ideal target to look for molecular signatures of past climatic events. We analysed mitochondrial DNA of specimens collected from the Antarctic continent and two Antarctic islands (AI) to infer past population processes and understand current genetic structure...
October 2017: Royal Society Open Science
https://www.readbyqxmd.com/read/29133028/evolution-and-postglacial-colonization-of-seewis-hantavirus-with-sorex-araneus-in-finland
#17
Jiaxin Ling, Teemu Smura, Daniel Tamarit, Otso Huitu, Liina Voutilainen, Heikki Henttonen, Antti Vaheri, Olli Vapalahti, Tarja Sironen
Hantaviruses have co-existed with their hosts for millions of years. Seewis virus (SWSV), a soricomorph-borne hantavirus, is widespread in Eurasia, ranging from Central Siberia to Western Europe. To gain insight into the phylogeography and evolutionary history of SWSV in Finland, lung tissue samples of 225 common shrews (Sorex araneus) trapped from different parts of Finland were screened for the presence of SWSV RNA. Forty-two of the samples were positive. Partial small (S), medium (M) and large (L) segments of the virus were sequenced, and analyzed together with all SWSV sequences available in Genbank...
November 10, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29131847/evolutionary-history-of-callose-synthases-in-terrestrial-plants-with-emphasis-on-proteins-involved-in-male-gametophyte-development
#18
Lenka Záveská Drábková, David Honys
Callose is a plant-specific polysaccharide (β-1,3-glucan) playing an important role in angiosperms in many developmental processes and responses to biotic and abiotic stresses. Callose is synthesised at the plasma membrane of plant cells by callose synthase (CalS) and, among others, represents the main polysaccharide in the callose wall surrounding the tetrads of developing microspores and in the growing pollen tube wall. CalS proteins involvement in spore development is a plesiomorphic feature of terrestrial plants, but very little is known about their evolutionary origin and relationships amongst the members of this protein family...
2017: PloS One
https://www.readbyqxmd.com/read/29131388/saccharomyces-interspecies-hybrids-as-model-organisms-for-studying-yeast-adaptation-to-stressful-environments
#19
Ksenija Lopandic
The strong development of molecular biology techniques and next-generation sequencing technologies in the last two decades has significantly improved our understanding of the evolutionary history of Saccharomyces yeasts. It has been shown that many strains isolated from man-made environments are not pure genetic lines, but contain genetic materials from different species that substantially increase their genome complexity. A number of strains have been described as interspecies hybrids, implying different yeast species that under specific circumstances exchange and recombine their genomes...
November 13, 2017: Yeast
https://www.readbyqxmd.com/read/29130975/karyotypes-versus-genomes-the-nymphalid-butterflies-melitaea-cinxia-danaus-plexippus-and-d-chrysippus
#20
Walther Traut, Virpi Ahola, David A S Smith, Ian J Gordon, Richard H Ffrench-Constant
The number of sequenced lepidopteran genomes is increasing rapidly. However, the corresponding assemblies rarely represent whole chromosomes and generally also lack the highly repetitive W sex chromosome. Knowledge of the karyotypes can facilitate genome assembly and further our understanding of sex chromosome evolution in Lepidoptera. Here, we describe the karyotypes of the Glanville fritillary Melitaea cinxia (n = 31), the monarch Danaus plexippus (n = 30), and the African queen D. chrysippus (2n = 60 or 59, depending on the source population)...
November 2, 2017: Cytogenetic and Genome Research
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