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Human evolutionary genetics

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https://www.readbyqxmd.com/read/28538728/the-sunflower-genome-provides-insights-into-oil-metabolism-flowering-and-asterid-evolution
#1
Hélène Badouin, Jérôme Gouzy, Christopher J Grassa, Florent Murat, S Evan Staton, Ludovic Cottret, Christine Lelandais-Brière, Gregory L Owens, Sébastien Carrère, Baptiste Mayjonade, Ludovic Legrand, Navdeep Gill, Nolan C Kane, John E Bowers, Sariel Hubner, Arnaud Bellec, Aurélie Bérard, Hélène Bergès, Nicolas Blanchet, Marie-Claude Boniface, Dominique Brunel, Olivier Catrice, Nadia Chaidir, Clotilde Claudel, Cécile Donnadieu, Thomas Faraut, Ghislain Fievet, Nicolas Helmstetter, Matthew King, Steven J Knapp, Zhao Lai, Marie-Christine Le Paslier, Yannick Lippi, Lolita Lorenzon, Jennifer R Mandel, Gwenola Marage, Gwenaëlle Marchand, Elodie Marquand, Emmanuelle Bret-Mestries, Evan Morien, Savithri Nambeesan, Thuy Nguyen, Prune Pegot-Espagnet, Nicolas Pouilly, Frances Raftis, Erika Sallet, Thomas Schiex, Justine Thomas, Céline Vandecasteele, Didier Varès, Felicity Vear, Sonia Vautrin, Martin Crespi, Brigitte Mangin, John M Burke, Jérôme Salse, Stéphane Muños, Patrick Vincourt, Loren H Rieseberg, Nicolas B Langlade
The domesticated sunflower, Helianthus annuus L., is a global oil crop that has promise for climate change adaptation, because it can maintain stable yields across a wide variety of environmental conditions, including drought. Even greater resilience is achievable through the mining of resistance alleles from compatible wild sunflower relatives, including numerous extremophile species. Here we report a high-quality reference for the sunflower genome (3.6 gigabases), together with extensive transcriptomic data from vegetative and floral organs...
May 22, 2017: Nature
https://www.readbyqxmd.com/read/28533660/genes-emotions-and-gut-microbiota-the-next-frontier-for-the-gastroenterologist
#2
REVIEW
Arturo Panduro, Ingrid Rivera-Iñiguez, Maricruz Sepulveda-Villegas, Sonia Roman
Most medical specialties including the field of gastroenterology are mainly aimed at treating diseases rather than preventing them. Genomic medicine studies the health/disease process based on the interaction of the human genes with the environment. The gastrointestinal (GI) system is an ideal model to analyze the interaction between our genes, emotions and the gut microbiota. Based on the current knowledge, this mini-review aims to provide an integrated synopsis of this interaction to achieve a better understanding of the GI disorders related to bad eating habits and stress-related disease...
May 7, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/28533464/the-colours-of-humanity-the-evolution-of-pigmentation-in-the-human-lineage
#3
REVIEW
Nina G Jablonski, George Chaplin
Humans are a colourful species of primate, with human skin, hair and eye coloration having been influenced by a great variety of evolutionary forces throughout prehistory. Functionally naked skin has been the physical interface between the physical environment and the human body for most of the history of the genus Homo, and hence skin coloration has been under intense natural selection. From an original condition of protective, dark, eumelanin-enriched coloration in early tropical-dwelling Homo and Homo sapiens, loss of melanin pigmentation occurred under natural selection as Homo sapiens dispersed into non-tropical latitudes of Africa and Eurasia...
July 5, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28530655/a-quantitative-and-multiplexed-approach-to-uncover-the-fitness-landscape-of-tumor-suppression-in-vivo
#4
Zoë N Rogers, Christopher D McFarland, Ian P Winters, Santiago Naranjo, Chen-Hua Chuang, Dmitri Petrov, Monte M Winslow
Cancer growth is a multistage, stochastic evolutionary process. While cancer genome sequencing has been instrumental in identifying the genomic alterations that occur in human tumors, the consequences of these alterations on tumor growth remain largely unexplored. Conventional genetically engineered mouse models enable the study of tumor growth in vivo, but they are neither readily scalable nor sufficiently quantitative to unravel the magnitude and mode of action of many tumor-suppressor genes. Here, we present a method that integrates tumor barcoding with ultradeep barcode sequencing (Tuba-seq) to interrogate tumor-suppressor function in mouse models of human cancer...
May 22, 2017: Nature Methods
https://www.readbyqxmd.com/read/28529975/phylogenetic-analyses-suggest-that-factors-other-than-the-capsid-protein-play-a-role-in-the-epidemic-potential-of-gii-2-norovirus
#5
Kentaro Tohma, Cara J Lepore, Lauren A Ford-Siltz, Gabriel I Parra
Norovirus is the leading cause of acute gastroenteritis worldwide. For over two decades, a single genotype (GII.4) has been responsible for most norovirus-associated cases. However, during the winter of 2014 to 2015, the GII.4 strains were displaced by a rarely detected genotype (GII.17) in several countries of the Asian continent. Moreover, during the winter of 2016 to 2017, the GII.2 strain reemerged as predominant in different countries worldwide. This reemerging GII.2 strain is a recombinant virus that presents a GII...
May 2017: MSphere
https://www.readbyqxmd.com/read/28527409/molecular-characterization-of-pigeon-torque-teno-virus-pttv-in-jiangsu-province
#6
Zhicheng Zhang, Wei Dai, Dingzhen Dai
The torque teno virus (TTV) is a recently discovered DNA virus that has been detected in many different hosts, including humans, livestock and poultry. To date, there is no report of pigeon TTV (PTTV) from anywhere in the world. To investigate the distribution of PTTV in pigeons from the eastern Chinese province of Jiangsu and characterize their genomes, we employed PCR to detect PTTV in 144 samples collected from 6 pigeon plants in Jiangsu province, amplify complete genomes from representative samples and analyze genetic characteristics using bioinformatics...
May 6, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28525990/transversions-have-larger-regulatory-effects-than-transitions
#7
Cong Guo, Ian C McDowell, Michael Nodzenski, Denise M Scholtens, Andrew S Allen, William L Lowe, Timothy E Reddy
BACKGROUND: Transversions (Tv's) are more likely to alter the amino acid sequence of proteins than transitions (Ts's), and local deviations in the Ts:Tv ratio are indicative of evolutionary selection on genes. Whether the two different types of mutations have different effects in non-protein-coding sequences remains unknown. Genetic variants primarily impact gene expression by disrupting the binding of transcription factors (TFs) and other DNA-binding proteins. Because Tv's cause larger changes in the shape of a DNA backbone, we hypothesized that Tv's would have larger impacts on TF binding and gene expression...
May 19, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28525953/human-yeast-hybrids-new-visions-to-genetic-disorders-and-drug-discovery
#8
Najmeh Zarei, Vahid Khalaj
Yeast has been a very helpful organism for centuries, especially with respect to fermentation of sugars and production of bread. However, for an even longer time, yeast has been a distant relative of humans having diverged from a common ancestor, about one billion years ago. More than one third of the yeast genes have human counterparts, despite this evolutionary distance. Yeast and human orthologs perform the same or similar functions. Investigations have demonstrated that 9-92% of the amino acid sequences in similar human and yeast proteins overlap...
July 2017: Iranian Biomedical Journal
https://www.readbyqxmd.com/read/28520221/rap1b-is-an-effector-of-axin2-regulating-crosstalk-of-signaling-pathways-during-skeletal-development
#9
Takamitsu Maruyama, Ming Jiang, Alycia Abbott, H-M Ivy Yu, Qirong Huang, Magdalena Chrzanowska-Wodnicka, Emily I Chen, Wei Hsu
Recent identification and isolation of suture stem cells capable of long term self-renewal, clonal expanding and differentiating demonstrate their essential role in calvarial bone development, homeostasis and injury repair. These bona fide stem cells express high level of Axin2 and are able to mediate bone regeneration and repair in a cell autonomous fashion. The importance of Axin2 is further demonstrated by its genetic inactivation in mice causing skeletal deformities resembling craniosynostosis in humans...
May 18, 2017: Journal of Bone and Mineral Research: the Official Journal of the American Society for Bone and Mineral Research
https://www.readbyqxmd.com/read/28515781/evolutionary-restoration-potential-evaluated-through-the-use-of-a-trait-linked-genetic-marker
#10
Travis M Apgar, Devon E Pearse, Eric P Palkovacs
Human-driven evolution can impact the ecological role and conservation value of impacted populations. Most evolutionary restoration approaches focus on manipulating gene flow, but an alternative approach is to manipulate the selection regime to restore historical or desired trait values. Here we examined the potential utility of this approach to restore anadromous migratory behavior in coastal California steelhead trout (Oncorhynchus mykiss) populations. We evaluated the effects of natural and anthropogenic environmental variables on the observed frequency of alleles at a genomic marker tightly associated with migratory behavior across 39 steelhead populations from across California, USA...
June 2017: Evolutionary Applications
https://www.readbyqxmd.com/read/28515739/patterns-of-inter-chromosomal-gene-conversion-on-the-male-specific-region-of-the-human-y-chromosome
#11
REVIEW
Beniamino Trombetta, Eugenia D'Atanasio, Fulvio Cruciani
The male-specific region of the human Y chromosome (MSY) is characterized by the lack of meiotic recombination and it has long been considered an evolutionary independent region of the human genome. In recent years, however, the idea that human MSY did not have an independent evolutionary history begun to emerge with the discovery that inter-chromosomal gene conversion (ICGC) can modulate the genetic diversity of some portions of this genomic region. Despite the study of the dynamics of this molecular mechanism in humans is still in its infancy, some peculiar features and consequences of it can be summarized...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28511886/numtogenesis-as-a-mechanism-for-development-of-cancer
#12
REVIEW
Keshav K Singh, Aaheli Roy Choudhury, Hemant K Tiwari
Transfer of genetic material from cytoplasmic organelles to the nucleus, an ongoing process, has implications in evolution, aging, and human pathologies such as cancer. The transferred mitochondrial DNA (mtDNA) fragments in the nuclear genome are called nuclear mtDNA or NUMTs. We have named the process numtogenesis, defining the term as the transfer of mtDNA into the nuclear genome, or, less specifically, the transfer of mitochondria or mitochondrial components into the nucleus. There is increasing evidence of the involvement of NUMTs in human biology and pathology...
May 13, 2017: Seminars in Cancer Biology
https://www.readbyqxmd.com/read/28511559/migrating-microbes-what-pathogens-can-tell-us-about-population-movements-and-human-evolution
#13
Charlotte J Houldcroft, Jean-Baptiste Ramond, Riaan F Rifkin, Simon J Underdown
BACKGROUND: The biology of human migration can be observed from the co-evolutionary relationship with infectious diseases. While many pathogens are brief, unpleasant visitors to human bodies, others have the ability to become life-long human passengers. The story of a pathogen's genetic code may, therefore, provide insight into the history of its human host. The evolution and distribution of disease in Africa is of particular interest, because of the deep history of human evolution in Africa, the presence of a variety of non-human primates, and tropical reservoirs of emerging infectious diseases...
May 16, 2017: Annals of Human Biology
https://www.readbyqxmd.com/read/28508126/what-s-the-point-golden-and-labrador-retrievers-living-in-kennels-do-not-understand-human-pointing-gestures
#14
Biagio D'Aniello, Alessandra Alterisio, Anna Scandurra, Emanuele Petremolo, Maria Rosaria Iommelli, Massimo Aria
In many studies that have investigated whether dogs' capacities to understand human pointing gestures are aspects of evolutionary or developmental social competences, family-owned dogs have been compared to shelter dogs. However, for most of these studies, the origins of shelter dogs were unknown. Some shelter dogs may have lived with families before entering shelters, and from these past experiences, they may have learned to understand human gestures. Furthermore, there is substantial variation in the methodology and analytic approaches used in such studies (e...
May 15, 2017: Animal Cognition
https://www.readbyqxmd.com/read/28507097/gene-duplication-and-neo-functionalization-in-the-evolutionary-and-functional-divergence-of-metazoan-copper-transporters-ctr1-and-ctr2
#15
Brandon L Logeman, L Kent Wood, Jaekwon Lee, Dennis J Thiele
Copper is an essential element for proper organismal development and is involved in a range of processes including oxidative phosphorylation, neuropeptide maturation, and connective tissue maturation. The copper transporter (Ctr) family of integral membrane proteins is ubiquitously found in eukaryotes and mediates the high-affinity transport of Cu+ across both the plasma membrane and endomembranes. While mammalian Ctr1 functions as a Cu+ transporter for Cu acquisition and is essential for embryonic development, a homologous protein, Ctr2, has been proposed to function as a low-affinity Cu transporter, a lysosomal Cu exporter, or a regulator of Ctr1 activity, but its functional and evolutionary relationship to Ctr1 is unclear...
May 15, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28502018/evolutionary-processes-in-populations-of-cryptosporidium-inferred-from-gp60-sequence-data
#16
Juan C Garcia-R, David T S Hayman
Cryptosporidiosis is one of the most common human infectious diseases globally. The gp60 gene has been adopted as a key marker for molecular epidemiological investigations into this protozoan disease because of the capability to characterize genotypes and detect variants within Cryptosporidium species infecting humans. However, we know relatively little about the potential spatial and temporal variation in population demography that can be inferred from this gene beyond that it is recognized to be under selective pressure...
May 13, 2017: Parasitology Research
https://www.readbyqxmd.com/read/28500794/rapid-broad-scale-gene-expression-evolution-in-experimentally-harvested-fish-populations
#17
Silva Uusi-Heikkilä, Tiina Sävilammi, Erica Leder, Robert Arlinghaus, Craig R Primmer
Gene expression changes potentially play an important role in adaptive evolution under human-induced selection pressures but this has been challenging to demonstrate in natural populations. Fishing exhibits strong selection pressure against large body size, thus potentially inducing evolutionary changes in life-history and other traits that may be slowly reversible once fishing ceases. However, there is a lack of convincing examples regarding the speed and magnitude of fisheries-induced evolution and thus the relevant underlying molecular-level effects remain elusive...
May 13, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28495960/inferring-the-joint-demographic-history-of-multiple-populations-beyond-the-diffusion-approximation
#18
Julien Jouganous, Will Long, Aaron P Ragsdale, Simon Gravel
Understanding variation in allele frequencies across populations is a central goal of population genetics. Classical models for the distribution of allele frequencies, using forward simulation, coalescent theory, or the diffusion approximation, have been applied extensively for demographic inference, medical study design, and evolutionary studies. Here we propose a tractable model of ordinary differential equations for the evolution of allele frequencies that is closely related to the diffusion approximation but avoids many of its limitations and approximations...
May 11, 2017: Genetics
https://www.readbyqxmd.com/read/28493321/local-genes-for-local-bacteria-evidence-of-allopatry-in-the-genomes-of-transatlantic-campylobacter-populations
#19
Ben Pascoe, Guillaume Méric, Koji Yahara, Helen Wimalarathna, Susan Murray, Matthew D Hitchings, Emma L Sproston, Catherine D Carrillo, Eduardo N Taboada, Kerry K Cooper, Steven Huynh, Alison J Cody, Keith A Jolley, Martin C J Maiden, Noel D McCarthy, Xavier Didelot, Craig T Parker, Samuel K Sheppard
The genetic structure of bacterial populations can be related to geographical locations of isolation. In some species, there is a strong correlation between geographical distance and genetic distance, which can be caused by different evolutionary mechanisms. Patterns of ancient admixture in Helicobacter pylori can be reconstructed in concordance with past human migration, whereas in Mycobacterium tuberculosis it is the lack of recombination that causes allopatric clusters. In Campylobacter, analyses of genomic data and molecular typing have been successful in determining the reservoir host species, but not geographical origin...
May 10, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28487274/simplification-of-genotyping-techniques-of-the-abo-blood-type-experiment-and-exploration-of-population-genetics
#20
Hu Jian, Zhou Yiren, Ding Jialin, Wang Zhiyuan, Liu Ling, Wang Yekai, Lou Huiling, Qiao Shouyi, Wu Yanhua
The ABO blood type is one of the most common and widely used genetic traits in humans. Three glycosyltransferase-encoding gene alleles, I(A), I(B) and i, produce three red blood cell surface antigens, by which the ABO blood type is classified. By using the ABO blood type experiment as an ideal case for genetics teaching, we can easily introduce to the students several genetic concepts, including multiple alleles, gene interaction, single nucleotide polymorphism (SNP) and gene evolution. Herein we have innovated and integrated our ABO blood type genetics experiments...
May 20, 2017: Yi Chuan, Hereditas
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