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evolutionary genetics

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https://www.readbyqxmd.com/read/28454448/gnaq-mutation-r183q-as-a-potential-cause-of-familial-sturge-weber-syndrome-a-case-report
#1
Zhengyi Huang, Yuchi Li, Zengxia Zhao, Jun Hu, Xiaoxin Tong, Xuhui Chen, Shuyun Liu, Xiaonan Xu, Yongjun Tao, Tingting Wang, Xin Cheng, Yangyang Dai, Yaoting Gui, Jun Wu
Sturge-Weber syndrome (SWS) is a rare neurocutaneous disorder whose etiology remains unclear. To investigate the genetic contribution underlying this disease, the genetic variants of a 4-generation family with a history of SWS was analyzed in the present study. SWS was diagnosed in 3 of the family members (II-1, III-11 and IV-6). Sanger sequencing was performed to identify mutations in G protein subunit αq (GNAQ) and RAS p21 protein activator 1 exons in the 3 patients with SWS and other unaffected family members...
April 2017: Oncology Letters
https://www.readbyqxmd.com/read/28453569/molecular-exploration-of-hidden-diversity-in-the-indo-west-pacific-sciaenid-clade
#2
Pei-Chun Lo, Shu-Hui Liu, Siti Azizah Mohd Nor, Wei-Jen Chen
The family Sciaenidae, known as croakers or drums, is one of the largest perciform fish families. A recent multi-gene based study investigating the phylogeny and biogeography of global sciaenids revealed that the origin and early diversification of this family occurred in tropical America during the Late Oligocene-Early Miocene before undergoing range expansions to other seas including the Indo-West Pacific, where high species richness is observed. Despite this clarification of the overall evolutionary history of the family, knowledge of the taxonomy and phylogeny of sciaenid genera endemic to the Indo-West Pacific is still limited due to lack of a thorough survey of all taxa...
2017: PloS One
https://www.readbyqxmd.com/read/28448578/evolutionary-history-of-tibetans-inferred-from-whole-genome-sequencing
#3
Hao Hu, Nayia Petousi, Gustavo Glusman, Yao Yu, Ryan Bohlender, Tsewang Tashi, Jonathan M Downie, Jared C Roach, Amy M Cole, Felipe R Lorenzo, Alan R Rogers, Mary E Brunkow, Gianpiero Cavalleri, Leroy Hood, Sama M Alpatty, Josef T Prchal, Lynn B Jorde, Peter A Robbins, Tatum S Simonson, Chad D Huff
The indigenous people of the Tibetan Plateau have been the subject of much recent interest because of their unique genetic adaptations to high altitude. Recent studies have demonstrated that the Tibetan EPAS1 haplotype is involved in high altitude-adaptation and originated in an archaic Denisovan-related population. We sequenced the whole-genomes of 27 Tibetans and conducted analyses to infer a detailed history of demography and natural selection of this population. We detected evidence of population structure between the ancestral Han and Tibetan subpopulations as early as 44 to 58 thousand years ago, but with high rates of gene flow until approximately 9 thousand years ago...
April 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28448491/relevant-units-of-analysis-for-applied-and-basic-research-dealing-with-neglected-transmissible-diseases-the-predominant-clonal-evolution-model-of-pathogenic-microorganisms
#4
REVIEW
Michel Tibayrenc, Francisco J Ayala
The predominant clonal evolution (PCE) model seeks to formulate a common population genetics framework for all micropathogens (namely, parasitic protozoa, fungi and yeasts, bacteria, and viruses). It relies on a definition of clonality that is only based on population structure features (namely, strongly restrained genetic recombination). Its clear-cut properties make it of strong interest for applied and basic research, since it permits the definition of stable, clearly delimited units of analysis below the species level: clonal genotypes and discrete genetic subdivisions ("near-clades")...
April 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28447196/the-axon-degeneration-gene-sarm1-is-evolutionarily-distinct-from-other-tir-domain-containing-proteins
#5
Harsha Malapati, Spencer M Millen, William J Buchser
Many forms of neurodegenerative disease are characterized by Wallerian degeneration, an active program of axonal destruction. Recently, the important player which enacts Wallerian degeneration was discovered, the multidomain protein SARM1. Since the SARM1 protein has classically been thought of as an innate immune molecule, its role in Wallerian degeneration has raised questions on the evolutionary forces acting on it. Here, we synthesize a picture of SARM1's evolution through various organisms by examining the molecular and genetic changes of SARM1 and the genes around it...
April 26, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28446899/clonal-spread-of-16s-rrna-methyltransferase-producing-klebsiella-pneumoniae-st37-with-high-prevalence-of-esbls-from-companion-animals-in-china
#6
Jing Xia, Liang-Xing Fang, Ke Cheng, Guo-Hao Xu, Xi-Ran Wang, Xiao-Ping Liao, Ya-Hong Liu, Jian Sun
We screened 30 Klebsiella pneumoniae isolates from dogs and cats at a single animal hospital in Guangdong Province, China. Among them, 12 K. pneumoniae strains possessed high-level resistance to amikacin and gentamicin and these were screened for 16S rRNA methyltransferase (16S-RMTase) genes. And then the genes positive isolates were detected for ESBLs (extended spectrum β-lactamases) and analyzed by pulsed-field gel electrophoresis, multilocus sequence typing, PCR-based replicon typing and plasmid analysis...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28446692/linking-species-habitat-and-past-palaeoclimatic-events-to-evolution-of-the-teleost-innate-immune-system
#7
Monica Hongrø Solbakken, Kjetil Lysne Voje, Kjetill Sigurd Jakobsen, Sissel Jentoft
Host-intrinsic factors as well as environmental changes are known to be strong evolutionary drivers defining the genetic foundation of immunity. Using a novel set of teleost genomes and a time-calibrated phylogeny, we here investigate the family of Toll-like receptor (TLR) genes and address the underlying evolutionary processes shaping the diversity of the first-line defence. Our findings reveal remarkable flexibility within the evolutionary design of teleost innate immunity characterized by prominent TLR gene losses and expansions...
April 26, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28446150/signatures-of-co-evolutionary-host-pathogen-interactions-in-the-genome-of-the-entomopathogenic-nematode-steinernema-carpocapsae
#8
Mitzi Flores-Ponce, Miguel Vallebueno-Estrada, Eduardo González-Orozco, Hilda E Ramos-Aboites, J Noé García-Chávez, Nelson Simões, Rafael Montiel
BACKGROUND: The entomopathogenic nematode Steinernema carpocapsae has been used worldwide as a biocontrol agent for insect pests, making it an interesting model for understanding parasite-host interactions. Two models propose that these interactions are co-evolutionary processes in such a way that equilibrium is never reached. In one model, known as "arms race", new alleles in relevant genes are fixed in both host and pathogens by directional positive selection, producing recurrent and alternating selective sweeps...
April 26, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28445723/mosquitoes-transmit-unique-west-nile-virus-populations-during-each-feeding-episode
#9
Nathan D Grubaugh, Joseph R Fauver, Claudia Rückert, James Weger-Lucarelli, Selene Garcia-Luna, Reyes A Murrieta, Alex Gendernalik, Darci R Smith, Doug E Brackney, Gregory D Ebel
Arthropod-borne viruses (arboviruses), such as Zika virus, chikungunya virus, and West Nile virus (WNV), pose continuous threats to emerge and cause large epidemics. Often, these events are associated with novel virus variants optimized for local transmission that first arise as minorities within a host. Thus, the conditions that regulate the frequency of intrahost variants are important determinants of emergence. Here, we describe the dynamics of WNV genetic diversity during its transmission cycle. By temporally sampling saliva from individual mosquitoes, we demonstrate that virus populations expectorated by mosquitoes are highly diverse and unique to each feeding episode...
April 25, 2017: Cell Reports
https://www.readbyqxmd.com/read/28444439/back-to-the-future-part-2-post-mortem-assessment-and-evolutionary-role-of-the-bio-medicolegal-sciences
#10
REVIEW
Santo Davide Ferrara, Giovanni Cecchetto, Rossana Cecchi, Donata Favretto, Silke Grabherr, Takaki Ishikawa, Toshikazu Kondo, Massimo Montisci, Heidi Pfeiffer, Maurizio Rippa Bonati, Dina Shokry, Marielle Vennemann, Thomas Bajanowski
Part 2 of the review "Back to the Future" is dedicated to the evolutionary role of the bio-medicolegal sciences, reporting the historical profiles, the state of the art, and prospects for future development of the main related techniques and methods of the ancillary disciplines that have risen to the role of "autonomous" sciences, namely, Genetics and Genomics, Toxicology, Radiology, and Imaging, involved in historic synergy in the "post-mortem assessment," together with the mother discipline Legal Medicine, by way of its primary fundament, universally denominated as Forensic Pathology...
April 25, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28444435/genetic-sex-determination-in-astatotilapia-calliptera-a-prototype-species-for-the-lake-malawi-cichlid-radiation
#11
Erin N Peterson, Maggie E Cline, Emily C Moore, Natalie B Roberts, Reade B Roberts
East African cichlids display extensive variation in sex determination systems. The species Astatotilapia calliptera is one of the few cichlids that reside both in Lake Malawi and in surrounding waterways. A. calliptera is of interest in evolutionary studies as a putative immediate outgroup species for the Lake Malawi species flock and possibly as a prototype ancestor-like species for the radiation. Here, we use linkage mapping to test association of sex in A. calliptera with loci that have been previously associated with genetic sex determination in East African cichlid species...
June 2017: Die Naturwissenschaften
https://www.readbyqxmd.com/read/28444297/rapid-and-parallel-adaptive-evolution-of-the-visual-system-of-neotropical-midas-cichlid-fishes
#12
Julián Torres-Dowdall, Michele E R Pierotti, Andreas Härer, Nidal Karagic, Joost M Woltering, Frederico Henning, Kathryn R Elmer, Axel Meyer
Midas cichlid fish are a Central American species flock containing 13 described species that has been dated to only few thousand years old, a historical timescale infrequently associated with speciation. Their radiation involved the colonization of several clear water crater lakes from two turbid great lakes. Therefore, Midas cichlids have been subjected to widely varying photic conditions during their radiation. Being a primary signal relay for information from the environment to the organism, the visual system is under continuing selective pressure and a prime organ system for accumulating adaptive changes during speciation, particularly in the case of dramatic shifts in photic conditions...
April 21, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28444200/the-mediterranean-the-cradle-of-anthoxanthum-poaceae-diploid-diversity
#13
Zuzana Chumová, Eliška Záveská, Terezie Mandáková, Karol Krak, Pavel Trávnícek
Background and Aims: Knowledge of diploid phylogeny and ecogeography provide a foundation for understanding plant evolutionary history, diversification patterns and taxonomy. The genus Anthoxanthum (vernal grasses, Poaceae) represents a taxonomically intricate polyploid complex with large phenotypic variation and poorly resolved evolutionary relationships. The aims of the study were to reveal: (1) evolutionary lineages of the diploid taxa and their genetic differentiation; (2) the past distribution of the rediscovered 'Mediterranean diploid'; and (3) possible migration routes of diploids in the Mediterranean...
April 21, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28442558/gene-flow-ancient-polymorphism-and-ecological-adaptation-shape-the-genomic-landscape-of-divergence-among-darwin-s-finches
#14
Fan Han, Sangeet Lamichhaney, B Rosemary Grant, Peter R Grant, Leif Andersson, Matthew T Webster
Genomic comparisons of closely related species have identified "islands" of locally elevated sequence divergence. Genomic islands may contain functional variants involved in local adaptation or reproductive isolation and may therefore play an important role in the speciation process. However, genomic islands can also arise through evolutionary processes unrelated to speciation, and examination of their properties can illuminate how new species evolve. Here, we performed scans for regions of high relative divergence (FST) in 12 species pairs of Darwin's finches at different genetic distances...
April 25, 2017: Genome Research
https://www.readbyqxmd.com/read/28442158/diversity-and-evolutionary-aspects-of-mucin-binding-mucbp-domain-repeats-among-lactobacillus-plantarum-group-strains-through-comparative-genetic-analysis
#15
Sundru Manjulata Devi, Prakash M Halami
Mucin binding protein (Mub) of Lactobacillus plantarum- group (LPG) is considered as a potential marker gene due to its diversity and adherence property to host intestinal layer. We recently observed strain specific diversity in mub gene of LPG strains (n=8) and grouped them into Type I, II and III based on the insertion and/or deletion of MucBP domain repeats (Devi et al., 2016). The mub gene expression pattern noted by real-time PCR revealed 67.64 increased fold change in MTCC 9483 with four MucBP repeats...
April 12, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/28440912/performance-of-in-silico-tools-for-the-evaluation-of-p16ink4a-cdkn2a-variants-in-cagi
#16
Marco Carraro, Giovanni Minervini, Manuel Giollo, Yana Bromberg, Emidio Capriotti, Rita Casadio, Roland Dunbrack, Lisa Elefanti, Pietro Fariselli, Carlo Ferrari, Julian Gough, Panagiotis Katsonis, Emanuela Leonardi, Olivier Lichtarge, Chiara Menin, Pier Luigi Martelli, Abhishek Niroula, Lipika R Pal, Susanna Repo, Maria Chiara Scaini, Mauno Vihinen, Qiong Wei, Qifang Xu, Yuedong Yang, Yizhou Yin, Jan Zaucha, Huiying Zhao, Yaoqi Zhou, Steven E Brenner, John Moult, Silvio C E Tosatto
Correct phenotypic interpretation of variants of unknown significance for cancer-associated genes is a diagnostic challenge as genetic screenings gain in popularity in the next-generation sequencing era. The Critical Assessment of Genome Interpretation (CAGI) experiment aims to test and define the state of the art of genotype-phenotype interpretation. Here, we present the assessment of the CAGI p16INK4a challenge. Participants were asked to predict the effect on cellular proliferation of ten variants for the p16INK4a tumor suppressor, a cyclin-dependent kinase inhibitor encoded by the CDKN2A gene...
April 25, 2017: Human Mutation
https://www.readbyqxmd.com/read/28440562/the-evolvability-of-herkogamy-quantifying-the-evolutionary-potential-of-a-composite-trait
#17
Øystein H Opedal, Geir H Bolstad, Thomas F Hansen, W Scott Armbruster, Christophe Pélabon
Accurate estimates of trait evolvabilities are central to predicting the short-term evolutionary potential of populations, and hence their ability to adapt to changing environments. We quantify and evaluate the evolvability of herkogamy, the spatial separation of male and female structures in flowers, a key floral trait associated with variation in mating systems. We compiled genetic-variance estimates for herkogamy and related floral traits, computed evolvabilities, and compared these among trait groups and among species differing in their mating systems...
April 25, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28440220/rapid-evolution-of-the-human-mutation-spectrum
#18
Kelley Harris, Jonathan K Pritchard
DNA is a remarkably precise medium for copying and storing biological information. This high fidelity results from the action of hundreds of genes involved in replication, proofreading, and damage repair. Evolutionary theory suggests that in such a system, selection has limited ability to remove genetic variants that change mutation rates by small amounts or in specific sequence contexts. Consistent with this, using SNV variation as a proxy for mutational input, we report here that mutational spectra differ substantially among species, human continental groups and even some closely-related populations...
April 25, 2017: ELife
https://www.readbyqxmd.com/read/28439564/the-evolution-of-lifespan-and-age-dependent-cancer-risk
#19
Andrii I Rozhok, James DeGregori
The Armitage-Doll multi-stage model of carcinogenesis tremendously refocused cancer science by postulating that carcinogenesis is driven by a sequence of genetic changes in cells. Age-dependent cancer incidence thus has been explained in terms of the time necessary for oncogenic mutations to occur. While the multi-step nature of cancer evolution is well-supported by evidence, the mutation-centric theory is unable to explain a number of phenomena, such as the disproportion between cancer frequency and animal body size or the scaling of cancer incidence to animal lifespan...
October 2016: Trends in Cancer
https://www.readbyqxmd.com/read/28439010/cyclops-reveals-human-transcriptional-rhythms-in-health-and-disease
#20
Ron C Anafi, Lauren J Francey, John B Hogenesch, Junhyong Kim
Circadian rhythms modulate many aspects of physiology. Knowledge of the molecular basis of these rhythms has exploded in the last 20 years. However, most of these data are from model organisms, and translation to clinical practice has been limited. Here, we present an approach to identify molecular rhythms in humans from thousands of unordered expression measurements. Our algorithm, cyclic ordering by periodic structure (CYCLOPS), uses evolutionary conservation and machine learning to identify elliptical structure in high-dimensional data...
April 24, 2017: Proceedings of the National Academy of Sciences of the United States of America
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