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"Evolutionary mechanisms"

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https://www.readbyqxmd.com/read/28225773/whole-genome-duplication-and-molecular-evolution-in-cornus-l-cornaceae-insights-from-transcriptome-sequences
#1
Yan Yu, Qiuyun Xiang, Paul S Manos, Douglas E Soltis, Pamela S Soltis, Bao-Hua Song, Shifeng Cheng, Xin Liu, Gane Wong
The pattern and rate of genome evolution have profound consequences in organismal evolution. Whole-genome duplication (WGD), or polyploidy, has been recognized as an important evolutionary mechanism of plant diversification. However, in non-model plants the molecular signals of genome duplications have remained largely unexplored. High-throughput transcriptome data from next-generation sequencing have set the stage for novel investigations of genome evolution using new bioinformatic and methodological tools in a phylogenetic framework...
2017: PloS One
https://www.readbyqxmd.com/read/28222092/the-genetic-basis-of-resistance-and-matching-allele-interactions-of-a-host-parasite-system-the-daphnia-magna-pasteuria-ramosa-model
#2
Gilberto Bento, Jarkko Routtu, Peter D Fields, Yann Bourgeois, Louis Du Pasquier, Dieter Ebert
Negative frequency-dependent selection (NFDS) is an evolutionary mechanism suggested to govern host-parasite coevolution and the maintenance of genetic diversity at host resistance loci, such as the vertebrate MHC and R-genes in plants. Matching-allele interactions of hosts and parasites that prevent the emergence of host and parasite genotypes that are universally resistant and infective are a genetic mechanism predicted to underpin NFDS. The underlying genetics of matching-allele interactions are unknown even in host-parasite systems with empirical support for coevolution by NFDS, as is the case for the planktonic crustacean Daphnia magna and the bacterial pathogen Pasteuria ramosa...
February 21, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28219972/venomics-integrative-venom-proteomics-and-beyond
#3
REVIEW
Juan J Calvete
Venoms are integrated phenotypes that evolved independently in, and are used for predatory and defensive purposes by, a wide phylogenetic range of organisms. The same principles that contribute to the evolutionary success of venoms, contribute to making the study of venoms of great interest in such diverse fields as evolutionary ecology and biotechnology. Evolution is profoundly contingent, and nature also reinvents itself continuosly. Changes in a complex phenotypic trait, such as venom, reflect the influences of prior evolutionary history, chance events, and selection...
February 20, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28212437/the-nature-of-allometry-in-an-exaggerated-trait-the-postocular-flange-in-platyneuromus-weele-insecta-megaloptera
#4
Andrés Ramírez-Ponce, Gabriela Garfias-Lozano, Atilano Contreras-Ramos
The origin and function of exaggerated traits exhibited by a great number of species with sexual dimorphism remain largely unexplored. The usual model considered as the evolutionary mechanism for the development of these structures is sexual selection. The nature of growth of the postocular flange (POF) in three species of the dobsonfly genus Platyneuromus (Megaloptera, Corydalidae, Corydalinae) is analyzed to explore sexual size dimorphism and allometric scaling. Results involve positive allometry of POF in males of two species, and negative allometry in males of one species, in general with a female-biased sexual dimorphism...
2017: PloS One
https://www.readbyqxmd.com/read/28205599/network-growth-models-a-behavioural-basis-for-attachment-proportional-to-fitness
#5
Michael Bell, Supun Perera, Mahendrarajah Piraveenan, Michiel Bliemer, Tanya Latty, Chris Reid
Several growth models have been proposed in the literature for scale-free complex networks, with a range of fitness-based attachment models gaining prominence recently. However, the processes by which such fitness-based attachment behaviour can arise are less well understood, making it difficult to compare the relative merits of such models. This paper analyses an evolutionary mechanism that would give rise to a fitness-based attachment process. In particular, it is proven by analytical and numerical methods that in homogeneous networks, the minimisation of maximum exposure to node unfitness leads to attachment probabilities that are proportional to node fitness...
February 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28185554/evolution-of-transcriptional-networks-in-yeast-alternative-teams-of-transcriptional-factors-for-different-species
#6
Adriana Muñoz, Daniella Santos Muñoz, Aleksey Zimin, James A Yorke
BACKGROUND: The diversity in eukaryotic life reflects a diversity in regulatory pathways. Nocedal and Johnson argue that the rewiring of gene regulatory networks is a major force for the diversity of life, that changes in regulation can create new species. RESULTS: We have created a method (based on our new "ping-pong algorithm) for detecting more complicated rewirings, where several transcription factors can substitute for one or more transcription factors in the regulation of a family of co-regulated genes...
November 11, 2016: BMC Genomics
https://www.readbyqxmd.com/read/28185400/microdiversity-shapes-the-traits-niche-space-and-biogeography-of-microbial-taxa
#7
REVIEW
Alyse A Larkin, Adam C Martiny
With rapidly improving sequencing technologies, scientists have recently gained the ability to examine diverse microbial communities at high genomic resolution, revealing that both free-living and host-associated microbes partition their environment at fine phylogenetic scales. This "microdiversity," or closely related (>97% similar 16S rRNA gene) but ecologically and physiologically distinct sub-taxonomic groups, appears to be an intrinsic property of microorganisms. However, the functional implications of microdiversity as well as its effects on microbial biogeography are poorly understood...
February 10, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28181048/evolutionary-mechanism-and-biological-functions-of-8-mers-containing-cg-dinucleotide-in-yeast
#8
Yan Zheng, Hong Li, Yue Wang, Hu Meng, Qiang Zhang, Xiaoqing Zhao
The rules of k-mer non-random usage and the biological functions are worthy of special attention. Firstly, the article studied human 8-mer spectra and found that only the spectra of cytosine-guanine (CG) dinucleotide classification formed independent unimodal distributions when the 8-mers were classified into three subsets under 16 dinucleotide classifications. Secondly, the distribution rules were reproduced by other seven species including yeast, which showed that the evolution phenomenon had species universality...
February 9, 2017: Chromosome Research
https://www.readbyqxmd.com/read/28173627/genetic-architecture-and-balancing-selection-the-life-and-death-of-differentiated-variants
#9
Violaine Llaurens, Annabel Whibley, Mathieu Joron
Balancing selection describes any form of natural selection which results in the persistence of multiple variants of a trait at intermediate frequencies within populations. By offering up a snapshot of multiple co-occurring functional variants and their interactions, systems under balancing selection can reveal the evolutionary mechanisms favouring the emergence and persistence of adaptive variation in natural populations. We here focus on the mechanisms by which several functional variants for a given trait can arise, a process typically requiring multiple epistatic mutations...
February 7, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28165020/a-potent-synthetic-inorganic-antibiotic-with-activity-against-drug-resistant-pathogens
#10
Shelby Hubick, Arumugam Jayaraman, Alexander McKeen, Shelby Reid, Jane Alcorn, John Stavrinides, Brian T Sterenberg
The acronymously named "ESKAPE" pathogens represent a group of bacteria that continue to pose a serious threat to human health, not only due to their propensity for repeated emergence, but also due to their ability to "eskape" antibiotic treatment. The evolution of multi-drug resistance in these pathogens alone has greatly outpaced the development of new therapeutics, necessitating an alternative strategy for antibiotic development that considers the evolutionary mechanisms driving antibiotic resistance. In this study, we synthesize a novel inorganic antibiotic, phosphopyricin, which has antibiotic activity against the Gram-positive methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus faecium (VRE)...
February 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28161510/the-material-record-and-the-antiquity-of-language
#11
REVIEW
Ian Tattersall
One view of language origins sees it as ancient and selection-driven; the other as recent and emergent. Such disagreement occurs because language is ephemeral, detectable only by indirect proxies. Because internalized language and symbolic thought are tightly linked, the best archaeological proxies for language are symbolic objects. Nothing indicates convincingly that any hominid behaved symbolically prior to Homo sapiens, which originated 200 kyr ago but started behaving symbolically only 100 kyr later. Most probably the necessary neural underpinnings arose exaptively in the extensive developmental reorganization that gave rise to anatomically distinctive Homo sapiens, and were recruited subsequently via a necessarily behavioral stimulus...
February 1, 2017: Neuroscience and Biobehavioral Reviews
https://www.readbyqxmd.com/read/28160497/unusual-evolutionary-mechanisms-to-escape-effector-triggered-immunity-in-the-fungal-phytopathogen-leptosphaeria-maculans
#12
C Plissonneau, F Blaise, B Ollivier, M Leflon, J Carpezat, T Rouxel, M-H Balesdent
Leptosphaeria maculans is the fungus responsible for the stem canker disease of oilseed rape (Brassica napus). AvrLm3 and AvrLm4-7, two avirulence effector genes of L. maculans, are involved in an unusual relationship: AvrLm4-7 suppresses the Rlm3-mediated resistance. Here, we assessed AvrLm3 polymorphism in a collection of 235 L. maculans isolates. No field isolates exhibited deletion or inactivating mutations in AvrLm3, as observed for other L. maculans avirulence genes. Eleven isoforms of the AvrLm3 protein were found...
February 4, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28134436/frequency-and-maintenance-of-unreduced-gametes-in-natural-plant-populations-associations-with-reproductive-mode-life-history-and-genome-size
#13
Julia M Kreiner, Paul Kron, Brian C Husband
Fertilization involving unreduced (2n) gametes is considered the dominant mechanism of polyploid formation in angiosperms; however, our knowledge of the prevalence of and evolutionary mechanisms maintaining 2n gametes in natural populations is limited. We hypothesize that 2n gametes are deleterious consequences of meiotic errors maintained by mutation-selection balance and should increase in species with relaxed opportunities for selection on sexual processes (asexuality), reduced efficacy of selection (asexuality, selfing) and increased genome instability (high chromosome number)...
January 30, 2017: New Phytologist
https://www.readbyqxmd.com/read/28133950/characterization-of-giant-modular-pkss-provides-insight-into-genetic-mechanism-for-structural-diversification-of-aminopolyol-polyketides
#14
Lihan Zhang, Takuya Hashimoto, Bin Qin, Junko Hashimoto, Ikuko Kozone, Teppei Kawahara, Masahiro Okada, Takayoshi Awakawa, Takuya Ito, Yoshinori Asakawa, Masashi Ueki, Shunji Takahashi, Hiroyuki Osada, Toshiyuki Wakimoto, Haruo Ikeda, Kazuo Shin-Ya, Ikuro Abe
Polyketides form many clinically valuable compounds. However, manipulation of their biosynthesis remains highly challenging. An understanding of gene cluster evolution provides a rationale for reprogramming of the biosynthetic machinery. Herein, we report characterization of giant modular polyketide synthases (PKSs) responsible for the production of aminopolyol polyketides. Heterologous expression of over 150 kbp polyketide gene clusters successfully afforded their products, whose stereochemistry was established by taking advantage of bioinformatic analysis...
February 6, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28128447/trpc2-pseudogenization-dynamics-in-bats-reveal-ancestral-vomeronasal-signaling-then-pervasive-loss
#15
Laurel R Yohe, Ramatu Abubakar, Christina Giordano, Elizabeth Dumont, Karen Sears, Stephen J Rossiter, Liliana M Dávalos
Comparative methods are often used to infer loss or gain of complex phenotypes, but few studies take advantage of genes tightly linked with complex traits to test for shifts in the strength of selection. In mammals vomerolfaction detects chemical cues mediating many social and reproductive behaviors and is highly conserved, but all bats exhibit degraded vomeronasal structures with the exception of two families (Phyllostomidae and Miniopteridae). These families either regained vomerolfaction after ancestral loss, or there were many independent losses after diversification from an ancestor with functional vomerolfaction...
January 27, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28098220/comparative-transcriptome-analysis-of-raccoon-dog-skin-to-determine-melanin-content-in-hair-and-melanin-distribution-in-skin
#16
Zhanyu Du, Kai Huang, Jiaping Zhao, Xingchao Song, Xiumei Xing, Qiong Wu, Linbo Zhang, Chao Xu
The raccoon dog (Nyctereutes procyonoides) is an important canid fur-bearing animal species worldwide. Chinese raccoon dogs that present a white mutation, especially those with a white coat. Exploring melanin biosynthesis in the hair and skin of raccoon dogs is important for understanding the survival and evolutionary mechanisms of them. In this study, we measured the content of melanin in the hair of two types of raccoon dog and generated stained slices of skin tissue. The results indicated that melanin biosynthesis occurs in the wild-type (W) and white-type (B) raccoon dog skin, although less melanin is produced in B skin...
January 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28096403/crystal-structure-of-pistol-a-class-of-self-cleaving-ribozyme
#17
Laura A Nguyen, Jimin Wang, Thomas A Steitz
Small self-cleaving ribozymes have been discovered in all evolutionary domains of life. They can catalyze site-specific RNA cleavage, and as a result, they have relevance in gene regulation. Comparative genomic analysis has led to the discovery of a new class of small self-cleaving ribozymes named Pistol. We report the crystal structure of Pistol at 2.97-Å resolution. Our results suggest that the Pistol ribozyme self-cleavage mechanism likely uses a guanine base in the active site pocket to carry out the phosphoester transfer reaction...
January 31, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28080995/rapid-emergence-of-pathogens-in-agro-ecosystems-global-threats-to-agricultural-sustainability-and-food-security
#18
REVIEW
Bruce A McDonald, Eva H Stukenbrock
Agricultural ecosystems are composed of genetically depauperate populations of crop plants grown at a high density and over large spatial scales, with the regional composition of crop species changing little from year to year. These environments are highly conducive for the emergence and dissemination of pathogens. The uniform host populations facilitate the specialization of pathogens to particular crop cultivars and allow the build-up of large population sizes. Population genetic and genomic studies have shed light on the evolutionary mechanisms underlying speciation processes, adaptive evolution and long-distance dispersal of highly damaging pathogens in agro-ecosystems...
December 5, 2016: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28076419/stability-of-a-coevolving-host-parasite-system-peaks-at-intermediate-productivity
#19
Xin-Feng Zhao, Yi-Qi Hao, Quan-Guo Zhang
Habitat productivity may affect the stability of consumer-resource systems, through both ecological and evolutionary mechanisms. We hypothesize that coevolving consumer-resource systems show more stable dynamics at intermediate resource availability, while very low-level resource supply cannot support sufficiently large populations of resource and consumer species to avoid stochastic extinction, and extremely resource-rich environments may promote escalatory arms-race-like coevolution that can cause strong fluctuations in species abundance and even extinction of one or both trophic levels...
2017: PloS One
https://www.readbyqxmd.com/read/28052323/complex-dynamics-underlie-the-evolution-of-imperfect-wing-pattern-convergence-in-butterflies
#20
Susan D Finkbeiner, Adriana D Briscoe, Sean P Mullen
Adaptive radiation is characterized by rapid diversification that is strongly associated with ecological specialization. However, understanding the evolutionary mechanisms fueling adaptive diversification requires a detailed knowledge of how natural selection acts at multiple life-history stages. Butterflies within the genus Adelpha represent one of the largest and most diverse butterfly lineages in the Neotropics. Although Adelpha species feed on an extraordinary diversity of larval hosts, convergent evolution is widespread in this group, suggesting that selection for mimicry may contribute to adaptive divergence among species...
January 4, 2017: Evolution; International Journal of Organic Evolution
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