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evolutionary genetics

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https://www.readbyqxmd.com/read/29454026/adaptation-of-escherichia-coli-to-long-term-batch-culture-in-various-rich-media
#1
Lacey L Westphal, Jasmine Lau, Zuly Negro, Ivan J Moreno, Wazim Ismail Mohammed, Heewook Lee, Haixu Tang, Steven E Finkel, Karin E Kram
Experimental evolution studies have characterized the genetic strategies microbes utilize to adapt to their environments, mainly focusing on how microbes adapt to constant and/or defined environments. Using a system that incubates Escherichia coli in different complex media in long-term batch culture, we have focused on how heterogeneity and environment affects adaptive landscapes. In this system, there is no passaging of cells, and therefore genetic diversity is lost only through negative selection, without the experimentally-imposed bottlenecking common in other platforms...
February 14, 2018: Research in Microbiology
https://www.readbyqxmd.com/read/29453424/genetic-control-and-evolutionary-potential-of-a-constitutive-resistance-mechanism-against-the-spruce-budworm-choristoneura-fumiferana-in-white-spruce-picea-glauca
#2
Claudia Méndez-Espinoza, Geneviève J Parent, Patrick Lenz, André Rainville, Laurence Tremblay, Greg Adams, Andrew McCartney, Éric Bauce, John MacKay
Insect herbivory may drive evolution by selecting for trees with heritable resistance against defoliation. The spruce budworm (Choristoneura fumiferana, SBW) is a highly damaging forest insect pest that can affect population structure of white spruce (Picea glauca) in North America. Resistance against SBW was recently described in white spruce and was linked to three constitutive resistance biomarkers: the phenolic compounds piceol and pungenol, and expression of a beta-glucosidase encoding gene (Pgβglu-1)...
February 17, 2018: Heredity
https://www.readbyqxmd.com/read/29451715/transitions-in-sex-determination-and-sex-chromosomes-across-vertebrate-species
#3
Matthew W Pennell, Judith E Mank, Catherine L Peichel
Despite the prevalence of sexual reproduction across eukaryotes, there is a remarkable diversity of sex determination mechanisms. The underlying causes of this diversity remain unclear, and it is unknown if there are convergent trends in the directionality of turnover in sex determination mechanisms. We used the recently assembled Tree of Sex database to assess patterns in the evolution of sex determination systems in the remarkably diverse vertebrate clades of teleost fish, squamate reptiles, and amphibians...
February 16, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29451433/populations-of-phytophthora-rubi-show-little-differentiation-and-high-rates-of-migration-among-states-in-the-western-united-states
#4
Javier F Tabima, Michael D Coffey, Inga Zasada, Niklaus J Grünwald
Population genetics is a powerful tool to understand patterns and evolutionary processes that are involved in plant pathogen emergence and adaptation to agricultural ecosystems. We are interested in studying the population dynamics of Phytophthora rubi, the causal agent of Phytophthora root rot in raspberry. P. rubi is found in the western U.S., where the majority of the fresh and processed raspberries are produced. We used genotyping-by-sequencing to characterize genetic diversity in populations of P. rubi sampled in the U...
February 16, 2018: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/29449965/genetic-diversity-and-cross-species-transmission-of-kobuviruses-in-vietnam
#5
Lu Lu, Nguyen Van Dung, Alasdair Ivens, Carlijn Bogaardt, Aine O'Toole, Juliet E Bryant, Juan Carrique-Mas, Nguyen Van Cuong, Pham Hong Anh, Maia A Rabaa, Ngo Tri Tue, Guy E Thwaites, Stephen Baker, Peter Simmonds, Mark Ej Woolhouse
Cross-species transmission of viruses poses a sustained threat to public health. Due to increased contact between humans and other animal species the possibility exists for cross-species transmissions and ensuing disease outbreaks. By using conventional PCR amplification and next generation sequencing, we obtained 130 partial or full genome kobuvirus sequences from humans in a sentinel cohort in Vietnam and various mammalian hosts including bats, rodents, pigs, cats, and civets. The evolution of kobuviruses in different hosts was analysed using Bayesian phylogenetic methods...
January 2018: Virus Evolution
https://www.readbyqxmd.com/read/29449618/codon-based-co-occurrence-network-motifs-in-human-mitochondria
#6
Pramod Shinde, Camellia Sarkar, Sarika Jalan
The nucleotide polymorphism in the human mitochondrial genome (mtDNA) tolled by codon position bias plays an indispensable role in human population dispersion and expansion. Herein, genome-wide nucleotide co-occurrence networks were constructed using data comprised of five different geographical regions and around 3000 samples for each region. We developed a powerful network model to describe complex mitochondrial evolutionary patterns among codon and non-codon positions. We found evidence that the evolution of human mitochondria DNA is dominated by adaptive forces, particularly mutation and selection, which was supported by many previous studies...
February 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29449510/winter-color-polymorphisms-identify-global-hot-spots-for-evolutionary-rescue-from-climate-change
#7
L Scott Mills, Eugenia V Bragina, Alexander V Kumar, Marketa Zimova, Diana J R Lafferty, Jennifer Feltner, Brandon M Davis, Klaus Hackländer, Paulo C Alves, Jeffrey M Good, José Melo-Ferreira, Andreas Dietz, Alexei V Abramov, Natalia Lopatina, Kairsten Fay
Maintenance of biodiversity in a rapidly changing climate will depend on the efficacy of evolutionary rescue, whereby population declines due to abrupt environmental change are reversed by shifts in genetically driven adaptive traits. However, a lack of traits known to be under direct selection by anthropogenic climate change has limited the incorporation of evolutionary processes into global conservation efforts. In 21 vertebrate species, some individuals undergo a seasonal color molt from summer brown to winter white as camouflage against snow, while other individuals remain brown...
February 15, 2018: Science
https://www.readbyqxmd.com/read/29449410/conserved-microrna-targeting-reveals-preexisting-gene-dosage-sensitivities-that-shaped-amniote-sex-chromosome-evolution
#8
Sahin Naqvi, Daniel W Bellott, Kathy S Lin, David C Page
Mammalian X and Y Chromosomes evolved from an ordinary autosomal pair. Genetic decay of the Y led to X Chromosome inactivation (XCI) in females, but some Y-linked genes were retained during the course of sex chromosome evolution, and many X-linked genes did not become subject to XCI. We reconstructed gene-by-gene dosage sensitivities on the ancestral autosomes through phylogenetic analysis of microRNA (miRNA) target sites and compared these preexisting characteristics to the current status of Y-linked and X-linked genes in mammals...
February 15, 2018: Genome Research
https://www.readbyqxmd.com/read/29447366/parent-of-origin-dependent-gene-expression-in-male-and-female-schistosome-parasites
#9
Julien Kincaid-Smith, Marion A L Picard, Céline Cosseau, Jérôme Boissier, Dany Severac, Christoph Grunau, Eve Toulza
Schistosomes are the causative agents of schistosomiasis, a Neglected Tropical Disease affecting over 230 million people worldwide. Additionally to their major impact on human health, they are also models of choice in evolutionary biology. These parasitic flatworms are unique among the common hermaphroditic trematodes as they have separate sexes. This so-called « evolutionary scandal » displays a female heterogametic genetic sex-determination system (ZZ males and ZW females), as well as a pronounced adult sexual dimorphism...
February 12, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29446801/emergence-ecology-and-dispersal-of-the-pandemic-generating-vibrio-cholerae-lineage
#10
REVIEW
Mohammad T Islam, Munirul Alam, Yan Boucher
Although cholera is an ancient disease that first arose at least half a millennium ago, it remains a major health threat globally. Its pandemic form is caused by strains from a single lineage of the bacterium Vibrio cholerae. The ancestor of this lineage harbored several distinctive characteristics, the most notable being the O1 antigen polysaccharide. This lineage generated two biotypes, first Classical, responsible for six pandemics, and later El Tor, responsible for the seventh and ongoing pandemic. Just as El Tor replaced Classical as the main cause of outbreaks in the last fifty years, several variants of El Tor have evolved and displaced their predecessors worldwide...
September 2017: International Microbiology: the Official Journal of the Spanish Society for Microbiology
https://www.readbyqxmd.com/read/29446800/biology-of-vibrio-cholera-editorial-overview
#11
EDITORIAL
Felipe Cava
In this monographic issue, we have the pleasure to present contributions from six of the leading laboratories at the forefront of Vibrio cholerae genetics, ecology and evolution, together with a brief tribute by Diego Romero to Doctor Jaime Ferrán y Clua, a pioneering Spanish bacteriologist who developed the first vaccine against this pathogen. V. cholerae is a free-living aquatic bacterium that interacts with and infects a variety of organisms. In humans it causes cholera, the deadly diarrhoea that was responsible for millions of deaths during seven pandemics since 1817, and still thousands every year...
September 2017: International Microbiology: the Official Journal of the Spanish Society for Microbiology
https://www.readbyqxmd.com/read/29446460/a-multivariate-ecogeographic-analysis-of-macaque-craniodental-variation
#12
Nicole D S Grunstra, Philipp Mitteroecker, Robert A Foley
OBJECTIVES: To infer the ecogeographic conditions that underlie the evolutionary diversification of macaques, we investigated the within- and between-species relationships of craniodental dimensions, geography, and environment in extant macaque species. We studied evolutionary processes by contrasting macroevolutionary patterns, phylogeny, and within-species associations. MATERIALS AND METHODS: Sixty-three linear measurements of the permanent dentition and skull along with data about climate, ecology (environment), and spatial geography were collected for 711 specimens of 12 macaque species and analyzed by a multivariate approach...
February 15, 2018: American Journal of Physical Anthropology
https://www.readbyqxmd.com/read/29445920/phylogenetic-diversity-and-in-vitro-susceptibility-profiles-of-human-pathogenic-members-of-the-fusarium-fujikuroi-species-complex-isolated-from-south-india
#13
Ananya Tupaki-Sreepurna, Vijayakishore Thanneru, Sangeetha Natarajan, Savitri Sharma, Anjana Gopi, Murugan Sundaram, Anupma Jyoti Kindo
Availability of molecular methods, gene sequencing, and phylogenetic species recognition have led to rare fungi being recognized as opportunistic pathogens. Fungal keratitis and onychomycosis are fairly common mycoses in the tropics, especially among outdoor workers and enthusiasts. The frequently isolated etiological agents belong to genera Candida, Aspergillus, and Fusarium. Within the genus Fusarium, known to be recalcitrant to prolonged antifungal treatment and associated with poor outcome, members of the Fusarium solani species complex are reported to be most common, followed by members of the Fusarium oxysporum SC and the Fusarium fujikuroi SC (FFSC)...
February 14, 2018: Mycopathologia
https://www.readbyqxmd.com/read/29445617/pathogenic-leptospira-advances-in-understanding-the-molecular-pathogenesis-and-virulence
#14
REVIEW
Ciamak Ghazaei
Leptospirosis is a common zoonotic disease has emerged as a major public health problem, with developing countries bearing disproportionate burdens. Although the diverse range of clinical manifestations of the leptospirosis in humans is widely documented, the mechanisms through which the pathogen causes disease remain undetermined. In addition, leptospirosis is a much-neglected life-threatening disease although it is one of the most important zoonoses occurring in a diverse range of epidemiological distribution...
2018: Open Veterinary Journal
https://www.readbyqxmd.com/read/29445326/structure-function-studies-of-the-%C3%AE-4-subunit-reveal-evolutionary-loss-of-a-glyr-subtype-involved-in-startle-and-escape-responses
#15
Sophie Leacock, Parnayan Syed, Victoria M James, Anna Bode, Koichi Kawakami, Angelo Keramidas, Maximiliano Suster, Joseph W Lynch, Robert J Harvey
Inhibitory glycine receptors (GlyRs) are pentameric ligand-gated anion channels with major roles in startle disease/hyperekplexia (GlyR α1), cortical neuronal migration/autism spectrum disorder (GlyR α2), and inflammatory pain sensitization/rhythmic breathing (GlyR α3). However, the role of the GlyR α4 subunit has remained enigmatic, because the corresponding human gene ( GLRA4 ) is thought to be a pseudogene due to an in-frame stop codon at position 390 within the fourth membrane-spanning domain (M4). Despite this, a recent genetic study has implicated GLRA4 in intellectual disability, behavioral problems and craniofacial anomalies...
2018: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/29445022/whole-genome-duplication-and-transposable-element-proliferation-drive-genome-expansion-in-corydoradinae-catfishes
#16
Sarah Marburger, Markos A Alexandrou, John B Taggart, Simon Creer, Gary Carvalho, Claudio Oliveira, Martin I Taylor
Genome size varies significantly across eukaryotic taxa and the largest changes are typically driven by macro-mutations such as whole genome duplications (WGDs) and proliferation of repetitive elements. These two processes may affect the evolutionary potential of lineages by increasing genetic variation and changing gene expression. Here, we elucidate the evolutionary history and mechanisms underpinning genome size variation in a species-rich group of Neotropical catfishes (Corydoradinae) with extreme variation in genome size-0...
February 14, 2018: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/29444864/lineage-specific-gene-acquisition-or-loss-is-involved-in-interspecific-hybrid-sterility-in-rice
#17
Yohei Koide, Atsushi Ogino, Takanori Yoshikawa, Yuki Kitashima, Nozomi Saito, Yoshitaka Kanaoka, Kazumitsu Onishi, Yoshihiro Yoshitake, Takuji Tsukiyama, Hiroki Saito, Masayoshi Teraishi, Yoshiyuki Yamagata, Aiko Uemura, Hiroki Takagi, Yoriko Hayashi, Tomoko Abe, Yoshimichi Fukuta, Yutaka Okumoto, Akira Kanazawa
Understanding the genetic basis of reproductive barriers between species has been a central issue in evolutionary biology. The S 1 locus in rice causes hybrid sterility and is a major reproductive barrier between two rice species, Oryza sativa and Oryza glaberrima The O. glaberrima -derived allele (denoted S 1 g ) on the S 1 locus causes preferential abortion of gametes with its allelic alternative (denoted S 1 s ) in S 1 g / S 1 s heterozygotes. Here, we used mutagenesis and screening of fertile hybrid plants to isolate a mutant with an allele, S 1 mut , which does not confer sterility in the S 1 mut / S 1 g and S 1 mut / S 1 s hybrids...
February 14, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29443109/methods-for-staging-pupal-periods-and-measurement-of-wing-pigmentation-of-drosophila-guttifera
#18
Yuichi Fukutomi, Keiji Matsumoto, Noriko Funayama, Shigeyuki Koshikawa
Diversified species of Drosophila (fruit fly) provide opportunities to study mechanisms of development and genetic changes responsible for evolutionary changes. In particular, the adult stage is a rich source of morphological traits for interspecific comparison, including wing pigmentation comparison. To study developmental differences among species, detailed observation and appropriate staging are required for precise comparison. Here we describe protocols for staging of pupal periods and quantification of wing pigmentation in a polka-dotted fruit fly, Drosophila guttifera...
January 24, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29441061/profiling-of-human-molecular-pathways-affected-by-retrotransposons-at-the-level-of-regulation-by-transcription-factor-proteins
#19
Daniil Nikitin, Dmitry Penzar, Andrew Garazha, Maxim Sorokin, Victor Tkachev, Nicolas Borisov, Alexander Poltorak, Vladimir Prassolov, Anton A Buzdin
Endogenous retroviruses and retrotransposons also termed retroelements (REs) are mobile genetic elements that were active until recently in human genome evolution. REs regulate gene expression by actively reshaping chromatin structure or by directly providing transcription factor binding sites (TFBSs). We aimed to identify molecular processes most deeply impacted by the REs in human cells at the level of TFBS regulation. By using ENCODE data, we identified ~2 million TFBS overlapping with putatively regulation-competent human REs located in 5-kb gene promoter neighborhood (~17% of all TFBS in promoter neighborhoods; ~9% of all RE-linked TFBS)...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/29440529/missing-compared-to-what-revisiting-heritability-genes-and-culture
#20
Marcus W Feldman, Sohini Ramachandran
Standard models for the determination of phenotypes from genes are grounded in simple assumptions that are inherent in the modern evolutionary synthesis (MES), which was developed in the 1930s, 1940s and 1950s. The MES was framed in the context of Mendelian genetic transmission enhanced by the Fisherian view of the way discretely inherited genes determine continuously quantitative phenotypes. The statistical models that are used to estimate and interpret genetic contributions to human phenotypes-including behavioural traits-are constructed within the framework of the MES...
April 5, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
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