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Human evolutionary genetics

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https://www.readbyqxmd.com/read/28912838/phylogenomics-of-colombian-helicobacter-pylori-isolates
#1
Andrés Julián Gutiérrez-Escobar, Esperanza Trujillo, Orlando Acevedo, María Mercedes Bravo
BACKGROUND: During the Spanish colonisation of South America, African slaves and Europeans arrived in the continent with their corresponding load of pathogens, including Helicobacter pylori. Colombian strains have been clustered with the hpEurope population and with the hspWestAfrica subpopulation in multilocus sequence typing (MLST) studies. However, ancestry studies have revealed the presence of population components specific to H. pylori in Colombia. The aim of this study was to perform a thorough phylogenomic analysis to describe the evolution of the Colombian urban H...
2017: Gut Pathogens
https://www.readbyqxmd.com/read/28911204/enhanced-vulnerability-of-human-proteins-towards-disease-associated-inactivation-through-divergent-evolution
#2
Encarnación Medina-Carmona, Julian E Fuchs, Jose A Gavira, Noel Mesa-Torres, Jose L Neira, Eduardo Salido, Rogelio Palomino-Morales, Miguel Burgos, David J Timson, Angel L Pey
Human proteins are vulnerable towards disease-associated single amino acid replacements affecting protein stability and function. Interestingly, a few studies have shown that consensus amino acids from mammals or vertebrates can enhance protein stability when incorporated into human proteins. Here, we investigate yet unexplored relationships between the high vulnerability of human proteins towards disease-associated inactivation and recent evolutionary site-specific divergence of stabilizing amino acids. Using phylogenetic, structural and experimental analyses, we show that divergence from the consensus amino acids at several sites during mammalian evolution has caused local protein destabilization in two human proteins linked to disease: cancer-associated NQO1 and alanine:glyoxylate aminotransferase, mutated in primary hyperoxaluria type I...
September 15, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28910985/yeast-bacteria-competition-induced-new-metabolic-traits-through-large-scale-genomic-rearrangements-in-lachancea-kluyveri
#3
Nerve Zhou, Samuele Bottagisi, Michael Katz, Joseph Schacherer, Anne Friedrich, Zoran Gojkovic, Krishna B S Swamy, Wolfgang Knecht, Concetta Compagno, Jure Piškur
Large-scale chromosomal rearrangements are an important source of evolutionary novelty that may have reshaped the genomes of existing yeast species. They dramatically alter genome organization and gene expression fueling a phenotypic leap in response to environmental constraints. Although the emergence of such signatures of genetic diversity is thought to be associated with human exploitation of yeasts, less is known about the driving forces operating in natural habitats. Here we hypothesize that an ecological battlefield characteristic of every autumn when fruits ripen accounts for the genomic innovations in natural populations...
September 1, 2017: FEMS Yeast Research
https://www.readbyqxmd.com/read/28904201/heterogeneity-of-the-epstein-barr-virus-major-internal-repeat-reveals-evolutionary-mechanisms-of-ebv-and-a-functional-defect-in-the-prototype-ebv-strain-b95-8
#4
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
https://www.readbyqxmd.com/read/28899353/tissue-specific-dna-methylation-is-conserved-across-human-mouse-and-rat-and-driven-by-primary-sequence-conservation
#5
Jia Zhou, Renee L Sears, Xiaoyun Xing, Bo Zhang, Daofeng Li, Nicole B Rockweiler, Hyo Sik Jang, Mayank N K Choudhary, Hyung Joo Lee, Rebecca F Lowdon, Jason Arand, Brianne Tabers, C Charles Gu, Theodore J Cicero, Ting Wang
BACKGROUND: Uncovering mechanisms of epigenome evolution is an essential step towards understanding the evolution of different cellular phenotypes. While studies have confirmed DNA methylation as a conserved epigenetic mechanism in mammalian development, little is known about the conservation of tissue-specific genome-wide DNA methylation patterns. RESULTS: Using a comparative epigenomics approach, we identified and compared the tissue-specific DNA methylation patterns of rat against those of mouse and human across three shared tissue types...
September 12, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28898481/escape-from-predators-and-genetic-variance-in-birds
#6
Yiting Jiang, Anders Pape Møller
Predation is a common cause of death in numerous organisms, and a host of anti-predator defenses have evolved. Such defenses often have a genetic background as shown by significant heritability and micro-evolutionary responses towards weaker defenses in the absence of predators. Flight initiation distance (FID) is the distance at which an individual animal takes flight when approached by a human, and hence it reflects the life history compromise between risk of predation and the benefits of foraging. Here we analyzed FID in 128 species of birds in relation to three measures of genetic variation, band sharing coefficient for minisatellites, observed heterozygosity and inbreeding coefficient for microsatellites in order to test whether FID was positively correlated with genetic variation...
September 12, 2017: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/28894461/a-grey-wolf-optimizer-for-modular-granular-neural-networks-for-human-recognition
#7
Daniela Sánchez, Patricia Melin, Oscar Castillo
A grey wolf optimizer for modular neural network (MNN) with a granular approach is proposed. The proposed method performs optimal granulation of data and design of modular neural networks architectures to perform human recognition, and to prove its effectiveness benchmark databases of ear, iris, and face biometric measures are used to perform tests and comparisons against other works. The design of a modular granular neural network (MGNN) consists in finding optimal parameters of its architecture; these parameters are the number of subgranules, percentage of data for the training phase, learning algorithm, goal error, number of hidden layers, and their number of neurons...
2017: Computational Intelligence and Neuroscience
https://www.readbyqxmd.com/read/28890534/harnessing-ancient-genomes-to-study-the-history-of-human-adaptation
#8
REVIEW
Stephanie Marciniak, George H Perry
The past several years have witnessed an explosion of successful ancient human genome-sequencing projects, with genomic-scale ancient DNA data sets now available for more than 1,100 ancient human and archaic hominin (for example, Neandertal) individuals. Recent 'evolution in action' analyses have started using these data sets to identify and track the spatiotemporal trajectories of genetic variants associated with human adaptations to novel and changing environments, agricultural lifestyles, and introduced or co-evolving pathogens...
September 11, 2017: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/28889020/the-novel-aspergillus-fumigatus-mat1-2-4-mating-type-gene-is-required-for-mating-and-cleistothecia-formation
#9
Yidong Yu, Jorge Amich, Cornelia Will, Carly E Eagle, Paul S Dyer, Sven Krappmann
Sexual propagation accompanied by recombination and the formation of spore-containing fruiting bodies is a cornerstone of fungal genetics and biology. In the human pathogen Aspergillus fumigatus sexual identity has previously been shown to be determined by MAT1-1-1 or MAT1-2-1 genes which act as transcriptional regulators and are present within idiomorphs found at the MAT locus. We here report the identification and first characterization of a further novel gene, termed MAT1-2-4, that is present in the MAT1-2 idiomorph of A...
September 6, 2017: Fungal Genetics and Biology: FG & B
https://www.readbyqxmd.com/read/28883554/adaptive-mutations-of-neuraminidase-stalk-truncation-and-deglycosylation-confer-enhanced-pathogenicity-of-influenza-a-viruses
#10
Sehee Park, Jin Il Kim, Ilseob Lee, Joon-Yong Bae, Kirim Yoo, Misun Nam, Juwon Kim, Mee Sook Park, Ki-Joon Song, Jin-Won Song, Sun-Ho Kee, Man-Seong Park
It has been noticed that neuraminidase (NA) stalk truncation has arisen from evolutionary adaptation of avian influenza A viruses (IAVs) from wild aquatic birds to domestic poultry. We identified this molecular alteration after the adaptation of a 2009 pandemic H1N1 virus (pH1N1) in BALB/c mice. The mouse-adapted pH1N1 lost its eight consecutive amino acids including one potential N-linked glycosite from the NA stalk region. To explore the relationship of NA stalk truncation or deglycosylation with viral pathogenicity changes, we generated NA stalk mutant viruses on the pH1N1 backbone by reverse genetics...
September 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28882004/when-loss-of-function-is-loss-of-function-assessing-mutational-signatures-and-impact-of-loss-of-function-genetic-variants
#11
Kymberleigh A Pagel, Vikas Pejaver, Guan Ning Lin, Hyun-Jun Nam, Matthew Mort, David N Cooper, Jonathan Sebat, Lilia M Iakoucheva, Sean D Mooney, Predrag Radivojac
Motivation: Loss-of-function genetic variants are frequently associated with severe clinical phenotypes, yet many are present in the genomes of healthy individuals. The available methods to assess the impact of these variants rely primarily upon evolutionary conservation with little to no consideration of the structural and functional implications for the protein. They further do not provide information to the user regarding specific molecular alterations potentially causative of disease...
July 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28880965/multiple-evolutionary-origins-of-trypanosoma-evansi-in-kenya
#12
Christine M Kamidi, Norah P Saarman, Kirstin Dion, Paul O Mireji, Collins Ouma, Grace Murilla, Serap Aksoy, Achim Schnaufer, Adalgisa Caccone
Trypanosoma evansi is the parasite causing surra, a form of trypanosomiasis in camels and other livestock, and a serious economic burden in Kenya and many other parts of the world. Trypanosoma evansi transmission can be sustained mechanically by tabanid and Stomoxys biting flies, whereas the closely related African trypanosomes T. brucei brucei and T. b. rhodesiense require cyclical development in tsetse flies (genus Glossina) for transmission. In this study, we investigated the evolutionary origins of T. evansi...
September 7, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28878990/human-altruism-evolution-and-moral-philosophy
#13
William J FitzPatrick
This paper has two central aims. The first is to explore philosophical complications that arise when we move from (i) explaining the evolutionary origins of genetically influenced traits associated with human cooperation and altruism, to (ii) explaining present manifestations of human thought, feeling and behaviour involving cooperation and altruism. While the former need only appeal to causal factors accessible to scientific inquiry, the latter must engage also with a distinctive form of explanation, i.e. reason-giving explanation, which in turn raises important philosophical questions, the answers to which will affect the nature of the ultimate explanations of our moral beliefs and related actions...
August 2017: Royal Society Open Science
https://www.readbyqxmd.com/read/28878043/the-rapid-in-vivo-evolution-of-pseudomonas-aeruginosa-in-ventilator-associated-pneumonia-patients-leads-to-attenuated-virulence
#14
Ke Wang, Yi-Qiang Chen, May M Salido, Gurjeet S Kohli, Jin-Liang Kong, Hong-Jie Liang, Zi-Ting Yao, Yan-Tong Xie, Hua-Yu Wu, Shuang-Qi Cai, Daniela I Drautz-Moses, Aaron E Darling, Stephan C Schuster, Liang Yang, Yichen Ding
Pseudomonas aeruginosa is an opportunistic pathogen that causes severe airway infections in humans. These infections are usually difficult to treat and associated with high mortality rates. While colonizing the human airways, P. aeruginosa could accumulate genetic mutations that often lead to its better adaptability to the host environment. Understanding these evolutionary traits may provide important clues for the development of effective therapies to treat P. aeruginosa infections. In this study, 25 P. aeruginosa isolates were longitudinally sampled from the airways of four ventilator-associated pneumonia (VAP) patients...
September 2017: Open Biology
https://www.readbyqxmd.com/read/28877004/reciprocity-outperforms-conformity-to-promote-cooperation
#15
Angelo Romano, Daniel Balliet
Evolutionary psychologists have proposed two processes that could give rise to the pervasiveness of human cooperation observed among individuals who are not genetically related: reciprocity and conformity. We tested whether reciprocity outperformed conformity in promoting cooperation, especially when these psychological processes would promote a different cooperative or noncooperative response. To do so, across three studies, we observed participants' cooperation with a partner after learning (a) that their partner had behaved cooperatively (or not) on several previous trials and (b) that their group members had behaved cooperatively (or not) on several previous trials with that same partner...
August 1, 2017: Psychological Science
https://www.readbyqxmd.com/read/28873088/identifying-genetic-variants-that-affect-viability-in-large-cohorts
#16
Hakhamanesh Mostafavi, Tomaz Berisa, Felix R Day, John R B Perry, Molly Przeworski, Joseph K Pickrell
A number of open questions in human evolutionary genetics would become tractable if we were able to directly measure evolutionary fitness. As a step towards this goal, we developed a method to examine whether individual genetic variants, or sets of genetic variants, currently influence viability. The approach consists in testing whether the frequency of an allele varies across ages, accounting for variation in ancestry. We applied it to the Genetic Epidemiology Research on Adult Health and Aging (GERA) cohort and to the parents of participants in the UK Biobank...
September 2017: PLoS Biology
https://www.readbyqxmd.com/read/28864013/the-transformative-potential-of-an-integrative-approach-to-pregnancy
#17
Haley R Eidem, Kriston L McGary, John A Capra, Patrick Abbot, Antonis Rokas
BACKGROUND: Complex traits typically involve diverse biological pathways and are shaped by numerous genetic and environmental factors. Pregnancy-associated traits and pathologies are further complicated by extensive communication across multiple tissues in two individuals, interactions between two genomes-maternal and fetal-that obscure causal variants and lead to genetic conflict, and rapid evolution of pregnancy-associated traits across mammals and in the human lineage. Given the multi-faceted complexity of human pregnancy, integrative approaches that synthesize diverse data types and analyses harbor tremendous promise to identify the genetic architecture and environmental influences underlying pregnancy-associated traits and pathologies...
September 2017: Placenta
https://www.readbyqxmd.com/read/28855970/lactase-persistence-in-tunisia-as-a-result-of-admixture-with-other-mediterranean-populations
#18
Yosra Ben Halima, Rym Kefi, Marco Sazzini, Cristina Giuliani, Sara De Fanti, Chokri Nouali, Majdi Nagara, Giacomo Mengozzi, Sahar Elouej, Abdelmajid Abid, Henda Jamoussi, Lotfi Chouchane, Giovanni Romeo, Sonia Abdelhak, Donata Luiselli
BACKGROUND: The ability to digest lactose after weaning, namely, lactase persistence (LP), is encoded by polymorphisms in the MCM6 gene and varies widely in frequency among different human populations. Although, evolution of LP-related genetic variants was investigated in many groups of Sub-Saharan African, Middle Eastern, and European ancestry, only few studies have focused on populations from North Africa and no data are especially available from the Tunisian one. For this reason, there is an urgent need to investigate the frequency patterns at these loci in Tunisia since this adaptive trait is implicated in health...
2017: Genes & Nutrition
https://www.readbyqxmd.com/read/28855362/a-father-effect-explains-sex-ratio-bias
#19
Aurelio F Malo, Felipe Martinez-Pastor, Francisco Garcia-Gonzalez, Julián Garde, Jonathan D Ballou, Robert C Lacy
Sex ratio allocation has important fitness consequences, and theory predicts that parents should adjust offspring sex ratio in cases where the fitness returns of producing male and female offspring vary. The ability of fathers to bias offspring sex ratios has traditionally been dismissed given the expectation of an equal proportion of X- and Y-chromosome-bearing sperm (CBS) in ejaculates due to segregation of sex chromosomes at meiosis. This expectation has been recently refuted. Here we used Peromyscus leucopus to demonstrate that sex ratio is explained by an exclusive effect of the father, and suggest a likely mechanism by which male-driven sex-ratio bias is attained...
August 30, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28854222/rahu-is-a-mutant-allele-of-dnmt3c-encoding-a-dna-methyltransferase-homolog-required-for-meiosis-and-transposon-repression-in-the-mouse-male-germline
#20
Devanshi Jain, Cem Meydan, Julian Lange, Corentin Claeys Bouuaert, Christopher E Mason, Kathryn V Anderson, Scott Keeney
Transcriptional silencing by heritable cytosine-5 methylation is an ancient strategy to repress transposable elements. It was previously thought that mammals possess four DNA methyltransferase paralogs-Dnmt1, Dnmt3a, Dnmt3b and Dnmt3l-that establish and maintain cytosine-5 methylation. Here we identify a fifth paralog, Dnmt3c, that is essential for retrotransposon methylation and repression in the mouse male germline. From a phenotype-based forward genetics screen, we isolated a mutant mouse called 'rahu', which displays severe defects in double-strand-break repair and homologous chromosome synapsis during male meiosis, resulting in sterility...
August 30, 2017: PLoS Genetics
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