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evolutionary genetics

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https://www.readbyqxmd.com/read/28823016/de-novo-synthesis-of-linoleic-acid-in-multiple-collembola-species
#1
Miriama Malcicka, Joachim Ruther, Jacintha Ellers
Many ecological interactions in communities take place between consumers and the organisms they feed on. Continuous surplus of specific nutritional compounds in the diet may lead to evolutionary changes in the metabolic capacity of the consumer, leaving the biosynthesis of such compounds prone to genetic decay and render organisms auxotrophic. A nutrient that is essential to many organisms is the unsaturated fatty acid, linoleic acid (LA; 18:2n-6), which is important in the maintenance of cell membrane fluidity and as a precursor for signaling molecules...
August 19, 2017: Journal of Chemical Ecology
https://www.readbyqxmd.com/read/28822625/landscaping-crossover-interference-across-a-genome
#2
REVIEW
Lidan Sun, Jing Wang, Mengmeng Sang, Libo Jiang, Bingyu Zhao, Tangran Cheng, Qixiang Zhang, Rongling Wu
The evolutionary success of eukaryotic organisms crucially depends on the capacity to produce genetic diversity through reciprocal exchanges of each chromosome pair, or crossovers (COs), during meiosis. It has been recognized that COs arise more evenly across a given chromosome than at random. This phenomenon, termed CO interference, occurs pervasively in eukaryotes and may confer a selective advantage. We describe here a multipoint linkage analysis procedure for segregating families to quantify the strength of CO interference over the genome, and extend this procedure to illustrate the landscape of CO interference in natural populations...
August 16, 2017: Trends in Plant Science
https://www.readbyqxmd.com/read/28821769/patterns-of-transcriptional-parallelism-and-variation-in-the-developing-olfactory-system-of-drosophila-species
#3
Jia Wern Pan, Qingyun Li, Scott Barish, Sumie Okuwa, Songhui Zhao, Charles Soeder, Matthew Kanke, Corbin D Jones, Pelin Cayirlioglu Volkan
Organisms have evolved strikingly parallel phenotypes in response to similar selection pressures suggesting that there may be shared constraints limiting the possible evolutionary trajectories. For example, the behavioral adaptation of specialist Drosophila species to specific host plants can exhibit parallel changes in their adult olfactory neuroanatomy. We investigated the genetic basis of these parallel changes by comparing gene expression during the development of the olfactory system of two specialist Drosophila species to that of four other generalist species...
August 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28821669/transcriptomic-analysis-of-ribosome-bound-mrna-in-cortical-neurites-in-vivo
#4
Rebecca Ouwenga, Allison M Lake, David O'Brien, Amit Mogha, Adish Dani, Joseph D Dougherty
Localized translation in neurites helps regulate synaptic strength and development. Dysregulation of local translation is associated with many neurological disorders. However, due to technical limitations, study of this phenomenon has largely been limited to brain regions with laminar organization of dendrites such as the hippocampus or cerebellum. It has not been examined in the cortex, a region of importance for most neurological disorders, where dendrites of each neuronal population are densely intermingled with cell bodies of others...
August 8, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/28821588/accumulation-of-deleterious-mutations-during-bacterial-range-expansions
#5
Lars Bosshard, Isabelle Dupanloup, Olivier Tenaillon, Rémy Bruggmann, Martin Ackermann, Stephan Peischl, Laurent Excoffier
Recent theory predicts that the fitness of pioneer populations can decline when species expand their range, due to high rates of genetic drift on wave fronts making selection less efficient at purging deleterious variants. To test these predictions, we studied the fate of mutator bacteria expanding their range for 1650 generations on agar plates. In agreement with theory, we find that growth abilities of strains with a high mutation rate (HMR lines) decreased significantly over time, unlike strains with a lower mutation rate (LMR lines) that present 3-4 times fewer mutations...
August 16, 2017: Genetics
https://www.readbyqxmd.com/read/28821587/drift-induced-selection-between-male-and-female-heterogamety
#6
Carl Veller, Pavitra Muralidhar, George W A Constable, Martin A Nowak
Evolutionary transitions between male and female heterogamety are common in both vertebrates and invertebrates. Theoretical studies of these transitions have found that, when all genotypes are equally fit, continuous paths of intermediate equilibria link the two sex chromosome systems. This observation has led to a belief that neutral evolution along these paths can drive transitions, and that arbitrarily small fitness differences among sex chromosome genotypes can determine the system to which evolution leads...
August 16, 2017: Genetics
https://www.readbyqxmd.com/read/28821382/sex-linked-behavior-evolution-stability-and-variability
#7
REVIEW
Cordelia Fine, John Dupré, Daphna Joel
Common understanding of human sex-linked behaviors is that proximal mechanisms of genetic and hormonal sex, ultimately shaped by the differential reproductive challenges of ancestral males and females, act on the brain to transfer sex-linked predispositions across generations. Here, we extend the debate on the role of nature and nurture in the development of traits in the lifetime of an individual, to their role in the cross-generation transfer of traits. Advances in evolutionary theory that posit the environment as a source of trans-generational stability, and new understanding of sex effects on the brain, suggest that the cross-generation stability of sex-linked patterns of behavior are sometimes better explained in terms of inherited socioenvironmental conditions, with biological sex fostering intrageneration variability...
July 29, 2017: Trends in Cognitive Sciences
https://www.readbyqxmd.com/read/28821346/sex-linked-behavior-evolution-stability-and-variability
#8
REVIEW
Cordelia Fine, John Dupré, Daphna Joel
Common understanding of human sex-linked behaviors is that proximal mechanisms of genetic and hormonal sex, ultimately shaped by the differential reproductive challenges of ancestral males and females, act on the brain to transfer sex-linked predispositions across generations. Here, we extend the debate on the role of nature and nurture in the development of traits in the lifetime of an individual, to their role in the cross-generation transfer of traits. Advances in evolutionary theory that posit the environment as a source of trans-generational stability, and new understanding of sex effects on the brain, suggest that the cross-generation stability of sex-linked patterns of behavior are sometimes better explained in terms of inherited socioenvironmental conditions, with biological sex fostering intrageneration variability...
September 2017: Trends in Cognitive Sciences
https://www.readbyqxmd.com/read/28821183/improvement-of-the-threespine-stickleback-genome-using-a-hi-c-based-proximity-guided-assembly
#9
Catherine L Peichel, Shawn T Sullivan, Ivan Liachko, Michael A White
Scaffolding genomes into complete chromosome assemblies remains challenging even with the rapidly increasing sequence coverage generated by current next-generation sequence technologies. Even with scaffolding information, many genome assemblies remain incomplete. The genome of the threespine stickleback (Gasterosteus aculeatus), a fish model system in evolutionary genetics and genomics, is not completely assembled despite scaffolding with high-density linkage maps. Here, we first test the ability of a Hi-C based proximity-guided assembly (PGA) to perform a de novo genome assembly from relatively short contigs...
September 1, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/28820456/deciphering-single-nucleotide-polymorphisms-and-evolutionary-trends-in-isolates-of-the-cydia-pomonella-granulovirus
#10
Jörg T Wennmann, Pit Radtke, Karolin E Eberle, Gianpiero Gueli Alletti, Johannes A Jehle
Six complete genome sequences of Cydia pomonella granulovirus (CpGV) isolates from Mexico (CpGV-M and CpGV-M1), England (CpGV-E2), Iran (CpGV-I07 and CpGV-I12), and Canada (CpGV-S) were aligned and analyzed for genetic diversity and evolutionary processes. The selected CpGV isolates represented recently identified phylogenetic lineages of CpGV, namely, the genome groups A to E. The genomes ranged from 120,816 bp to 124,269 bp. Several common differences between CpGV-M, -E2, -I07, -I12 and -S to CpGV-M1, the first sequenced and published CpGV isolate, were highlighted...
August 18, 2017: Viruses
https://www.readbyqxmd.com/read/28820115/six-key-traits-of-fungi-their-evolutionary-origins-and-genetic-bases
#11
László G Nagy, Renáta Tóth, Enikő Kiss, Jason Slot, Attila Gácser, Gábor M Kovács
The fungal lineage is one of the three large eukaryotic lineages that dominate terrestrial ecosystems. They share a common ancestor with animals in the eukaryotic supergroup Opisthokonta and have a deeper common ancestry with plants, yet several phenotypes, such as morphological, physiological, or nutritional traits, make them unique among all living organisms. This article provides an overview of some of the most important fungal traits, how they evolve, and what major genes and gene families contribute to their development...
July 2017: Microbiology Spectrum
https://www.readbyqxmd.com/read/28818621/codon-usage-bias-in-the-n-gene-of-rabies-virus
#12
Wanting He, Hongyu Zhang, Yuchen Zhang, Ruyi Wang, Sijia Lu, Yanjie Ji, Chang Liu, Pengkun Yuan, Shuo Su
Since its emergence, rabies virus (RABV) has been a major worldwide concern especially in developing countries. The nucleoprotein (N) of RABV is highly conserved and key for genetic typing, thus a better understanding of the N gene evolutionary trajectory can assist the development of control measures. We found that the N gene of RABV has a low codon usage bias with a mean effective number of codons (ENC) value of 56.33 influenced by both mutation pressure and natural selection. However, neutrality analysis indicated that natural selection dominates over mutation pressure...
August 14, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28818345/mobile-group-ii-introns-as-ancestral-eukaryotic-elements
#13
REVIEW
Olga Novikova, Marlene Belfort
The duality of group II introns, capable of carrying out both self-splicing and retromobility reactions, is hypothesized to have played a profound role in the evolution of eukaryotes. These introns likely provided the framework for the emergence of eukaryotic retroelements, spliceosomal introns and other key components of the spliceosome. Group II introns are found in all three domains of life and are therefore considered to be exceptionally successful mobile genetic elements. Initially identified in organellar genomes, group II introns are found in bacteria, chloroplasts, and mitochondria of plants and fungi, but not in nuclear genomes...
August 14, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28818331/molecular-epidemiology-of-epizootic-haematopoietic-necrosis-virus-ehnv
#14
Paul M Hick, Kuttichantran Subramaniam, Patrick M Thompson, Thomas B Waltzek, Joy A Becker, Richard J Whittington
Low genetic diversity of Epizootic haematopoietic necrosis virus (EHNV) was determined for the complete genome of 16 isolates spanning the natural range of hosts, geography and time since the first outbreaks of disease. Genomes ranged from 125,591-127,487 nucleotides with 97.47% pairwise identity and 106-109 genes. All isolates shared 101 core genes with 121 potential genes predicted within the pan-genome of this collection. There was high conservation within 90,181 nucleotides of the core genes with isolates separated by average genetic distance of 3...
August 14, 2017: Virology
https://www.readbyqxmd.com/read/28817588/phylogeography-of-the-reticulated-python-malayopython-reticulatus-ssp-conservation-implications-for-the-worlds-most-traded-snake-species
#15
Gillian Murray-Dickson, Muhammad Ghazali, Rob Ogden, Rafe Brown, Mark Auliya
As an important economic natural resource in Southeast Asia, reticulated pythons (Malayopython reticulatus ssp.) are primarily harvested from the wild for their skins-which are prized in the luxury leather goods industry. Trade dynamics of this CITES Appendix II listed species are complex and management approaches on the country or regional level appear obscure. Little is known about the actual geographic point-of-harvest of snakes, how genetic diversity is partitioned across the species range, how current harvest levels may affect the genetic viability of populations, and whether genetic structure could (or should) be accounted for when managing harvest quotas...
2017: PloS One
https://www.readbyqxmd.com/read/28815929/aggregation-of-population-based-genetic-variation-over-protein-domain-homologues-and-its-potential-use-in-genetic-diagnostics
#16
Laurens Wiel, Hanka Venselaar, Joris A Veltman, Gerrit Vriend, Christian Gilissen
Whole exomes of patients with a genetic disorder are nowadays routinely sequenced but interpretation of the identified genetic variants remains a major challenge. The increased availability of population-based human genetic variation has given rise to measures of genetic tolerance that have been used, for example, to predict disease-causing genes in neurodevelopmental disorders. Here, we investigated whether combining variant information from homologous protein domains can improve variant interpretation. For this purpose, we developed a framework that maps population variation and known pathogenic mutations onto 2,750 "meta-domains"...
August 16, 2017: Human Mutation
https://www.readbyqxmd.com/read/28814792/genetic-regulatory-effects-modified-by-immune-activation-contribute-to-autoimmune-disease-associations
#17
Sarah Kim-Hellmuth, Matthias Bechheim, Benno Pütz, Pejman Mohammadi, Yohann Nédélec, Nicholas Giangreco, Jessica Becker, Vera Kaiser, Nadine Fricker, Esther Beier, Peter Boor, Stephane E Castel, Markus M Nöthen, Luis B Barreiro, Joseph K Pickrell, Bertram Müller-Myhsok, Tuuli Lappalainen, Johannes Schumacher, Veit Hornung
The immune system plays a major role in human health and disease, and understanding genetic causes of interindividual variability of immune responses is vital. Here, we isolate monocytes from 134 genotyped individuals, stimulate these cells with three defined microbe-associated molecular patterns (LPS, MDP, and 5'-ppp-dsRNA), and profile the transcriptomes at three time points. Mapping expression quantitative trait loci (eQTL), we identify 417 response eQTLs (reQTLs) with varying effects between conditions...
August 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/28814718/adaptive-and-non-adaptive-divergence-in-a-common-landscape
#18
Joost A M Raeymaekers, Anurag Chaturvedi, Pascal I Hablützel, Io Verdonck, Bart Hellemans, Gregory E Maes, Luc De Meester, Filip A M Volckaert
Species in a common landscape often face similar selective environments. The capacity of organisms to adapt to these environments may be largely species specific. Quantifying shared and unique adaptive responses across species within landscapes may thus improve our understanding of landscape-moderated biodiversity patterns. Here we test to what extent populations of two coexisting and phylogenetically related fishes-three-spined and nine-spined stickleback-differ in the strength and nature of neutral and adaptive divergence along a salinity gradient...
August 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/28814642/an-indel-in-the-promoter-of-al-activated-malate-transporter-9-selected-during-tomato-domestication-determines-fruit-malate-contents-and-aluminum-tolerance
#19
Jie Ye, Xin Wang, Ti Xu Hu, Feng Xia Zhang, Bing Wang, Chang Xin Li, Tian Xia Yang, Han Xia Li, Yong En Lu, James J Giovannoni, Yuyang Zhang, Zhibiao Ye
Deciphering the mechanism of malate accumulation in plants would contribute to a greater understanding of plant chemistry, which has implications for improving flavor quality in crop species and enhancing human health benefits. However, the regulation of malate metabolism is poorly understood in crops such as tomato (Solanum lycopersicum). Here, we integrated a metabolite-based genome-wide association study (mGWAS) with linkage mapping and gene functional studies to characterize the genetics of malate accumulation in a global collection of tomato accessions with broad genetic diversity...
August 16, 2017: Plant Cell
https://www.readbyqxmd.com/read/28814606/their-loss-is-our-gain-regressive-evolution-in-vertebrates-provides-genomic-models-for-uncovering-human-disease-loci
#20
REVIEW
Christopher A Emerling, Andrew D Widjaja, Nancy N Nguyen, Mark S Springer
Throughout Earth's history, evolution's numerous natural 'experiments' have resulted in a diverse range of phenotypes. Though de novo phenotypes receive widespread attention, degeneration of traits inherited from an ancestor is a very common, yet frequently neglected, evolutionary path. The latter phenomenon, known as regressive evolution, often results in vertebrates with phenotypes that mimic inherited disease states in humans. Regressive evolution of anatomical and/or physiological traits is typically accompanied by inactivating mutations underlying these traits, which frequently occur at loci identical to those implicated in human diseases...
August 16, 2017: Journal of Medical Genetics
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