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"Evolutionary history"

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https://www.readbyqxmd.com/read/29346646/the-evolutionary-history-of-nebraska-deer-mice-local-adaptation-in-the-face-of-strong-gene-flow
#1
Susanne P Pfeifer, Stefan Laurent, Vitor C Sousa, Catherine R Linnen, Matthieu Foll, Laurent Excoffier, Hopi E Hoekstra, Jeffrey D Jensen
The interplay of gene flow, genetic drift, and local selective pressure is a dynamic process that has been well studied from a theoretical perspective over the last century. Wright and Haldane laid the foundation for expectations under an island-continent model, demonstrating that an island-specific beneficial allele may be maintained locally if the selection coefficient is larger than the rate of migration of the ancestral allele from the continent. Subsequent extensions of this model have provided considerably more insight...
January 15, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29343599/the-evolution-of-tail-weaponization-in-amniotes
#2
Victoria M Arbour, Lindsay E Zanno
Weaponry, for the purpose of intraspecific combat or predator defence, is one of the most widespread animal adaptations, yet the selective pressures and constraints governing its phenotypic diversity and skeletal regionalization are not well understood. Here, we investigate the evolution of tail weaponry in amniotes, a rare form of weaponry that nonetheless evolved independently among a broad spectrum of life including mammals, turtles and dinosaurs. Using phylogenetic comparative methods, we test for links between morphology, ecology and behaviour in extant amniotes known to use the tail as a weapon, and in extinct taxa bearing osseous tail armaments...
January 31, 2018: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/29343558/postcranial-diversity-and-recent-ecomorphic-impoverishment-of-north-american-gray-wolves
#3
Susumu Tomiya, Julie A Meachen
Recent advances in genomics and palaeontology have begun to unravel the complex evolutionary history of the gray wolf, Canis lupus Still, much of their phenotypic variation across time and space remains to be documented. We examined the limb morphology of the fossil and modern North American gray wolves from the late Quaternary (<ca 70 ka) to better understand their postcranial diversity through time. We found that the late-Pleistocene gray wolves were characterized by short-leggedness on both sides of the Cordilleran-Laurentide ice sheets, and that this trait survived well into the Holocene despite the collapse of Pleistocene megafauna and disappearance of the 'Beringian wolf' from Alaska...
January 2018: Biology Letters
https://www.readbyqxmd.com/read/29340581/gene-turnover-and-diversification-of-the-%C3%AE-and-%C3%AE-globin-gene-families-in-sauropsid-vertebrates
#4
Federico G Hoffmann, Michael W Vandewege, Jay F Storz, Juan C Opazo
The genes that encode the α- and β-chain subunits of vertebrate hemoglobin have served as a model system for elucidating general principles of gene family evolution, but little is known about patterns of evolution in amniotes other than mammals and birds. Here we report a comparative genomic analysis of the α- and β-globin gene clusters in sauropsids (archosaurs and nonavian reptiles). The objectives were to characterize changes in the size and membership composition of the α- and β-globin gene families within and among the major sauropsid lineages, to reconstruct the evolutionary history of the sauropsid α- and β-globin genes, to resolve orthologous relationships, and to reconstruct evolutionary changes in the developmental regulation of gene expression...
January 11, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29340210/treetime-maximum-likelihood-phylodynamic-analysis
#5
Pavel Sagulenko, Vadim Puller, Richard A Neher
Mutations that accumulate in the genome of cells or viruses can be used to infer their evolutionary history. In the case of rapidly evolving organisms, genomes can reveal their detailed spatiotemporal spread. Such phylodynamic analyses are particularly useful to understand the epidemiology of rapidly evolving viral pathogens. As the number of genome sequences available for different pathogens has increased dramatically over the last years, phylodynamic analysis with traditional methods becomes challenging as these methods scale poorly with growing datasets...
January 2018: Virus Evolution
https://www.readbyqxmd.com/read/29335414/evolutionary-history-of-coleoptera-revealed-by-extensive-sampling-of-genes-and-species
#6
Shao-Qian Zhang, Li-Heng Che, Yun Li, Dan Liang, Hong Pang, Adam Ślipiński, Peng Zhang
Beetles (Coleoptera) are the most diverse and species-rich group of insects, and a robust, time-calibrated phylogeny is fundamental to understanding macroevolutionary processes that underlie their diversity. Here we infer the phylogeny and divergence times of all major lineages of Coleoptera by analyzing 95 protein-coding genes in 373 beetle species, including ~67% of the currently recognized families. The subordinal relationships are strongly supported as Polyphaga (Adephaga (Archostemata, Myxophaga)). The series and superfamilies of Polyphaga are mostly monophyletic...
January 15, 2018: Nature Communications
https://www.readbyqxmd.com/read/29331867/classification-and-evolution-of-human-papillomavirus-genome-variants-alpha-5-hpv26-51-69-82-alpha-6-hpv30-53-56-66-alpha-11-hpv34-73-alpha-13-hpv54-and-alpha-3-hpv61
#7
Zigui Chen, Mark Schiffman, Rolando Herrero, Rob DeSalle, Kathryn Anastos, Michel Segondy, Vikrant V Sahasrabuddhe, Patti E Gravitt, Ann W Hsing, Paul K S Chan, Robert D Burk
HPV variants from the same type can be classified into lineages and sublineages based on the complete genome differences and the phylogenetic topologies. We examined nucleotide variations of twelve HPV types within the species Alpha-5 (HPV26, 51, 69, 82), Alpha-6 (HPV30, 53, 56, 66), Alpha-11 (HPV34, 73), Alpha-13 (HPV54) and Alpha-3 (HPV61) by analyzing 1432 partial sequences and 181 complete genomes from multiple geographic populations. The inter-lineage and inter-sublineage mean differences of HPV variants ranged between 0...
January 11, 2018: Virology
https://www.readbyqxmd.com/read/29330664/an-iranian-genomic-sequence-of-beet-mosaic-virus-provides-insights-into-diversity-and-evolution-of-the-world-population
#8
Musa Mohammadi, Adrian J Gibbs, Ahmad Hosseini, Samin Hosseini
Beet mosaic virus (BtMV), the only Potyvirus known to infect sugar beet, occurs worldwide in beet crops. The full genome sequencing of a BtMV isolate from Iran (Ir-VRU), enabled us to better understand the evolutionary history of this virus. Selection analysis suggested that BtMV evolution is mainly under negative selection but its strength varies in different proteins with the multifunctional proteins under strongest selection. Recombination has played a major role in the evolution of the BtMVs; only the Ir-VRU and USA isolates show no evidence of recombination...
January 12, 2018: Virus Genes
https://www.readbyqxmd.com/read/29329524/uncovering-the-evolutionary-history-of-neo-xy-sex-chromosomes-in-the-grasshopper-ronderosia-bergii-orthoptera-melanoplinae-through-satellite-dna-analysis
#9
Octavio M Palacios-Gimenez, Diogo Milani, Bernardo Lemos, Elio R Castillo, Dardo A Martí, Erica Ramos, Cesar Martins, Diogo C Cabral-de-Mello
BACKGROUND: Neo-sex chromosome systems arose independently multiple times in evolution, presenting the remarkable characteristic of repetitive DNAs accumulation. Among grasshoppers, occurrence of neo-XY was repeatedly noticed in Melanoplinae. Here we analyzed the most abundant tandem repeats of R. bergii (2n = 22, neo-XY♂) using deep Illumina sequencing and graph-based clustering in order to address the neo-sex chromosomes evolution. RESULTS: The analyses revealed ten families of satDNAs comprising about ~1% of the male genome, which occupied mainly C-positive regions of autosomes...
January 8, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29329439/conserved-proteins-of-the-rna-interference-system-in-the-arbuscular-mycorrhizal-fungus-rhizoglomus-irregulare-provide-new-insight-into-the-evolutionary-history-of-glomeromycota
#10
Soon-Jae Lee, Mengxuan Kong, Paul Harrison, Mohamed Hijri
Horizontal gene transfer (HGT) is an important mechanism in the evolution of many living organisms particularly in Prokaryotes where genes are frequently dispersed between taxa. Although, HGT has been reported in Eukaryotes, its accumulative effect and its frequency has been questioned. Arbuscular mycorrhizal fungi (AMF) are an early diverged fungal lineage belonging to phylum Glomeromycota, whose phylogenetic position is still under debate. The history of AMF and land plant symbiosis dates back to at least 460 million years ago...
January 10, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29328532/population-genomic-footprints-of-host-adaptation-introgression-and-recombination-in-coffee-leaf-rust
#11
Diogo Nuno Silva, Vítor Várzea, Octávio Salgueiro Paulo, Dora Batista
Coffee Leaf Rust, caused by Hemileia vastatrix (Hv), represents the biggest threat to coffee production worldwide and ranks amongst the most serious fungal diseases in history. Despite a recent series of outbreaks and emergence of hyper-virulent strains, the population evolutionary history and potential of this pathogen remains poorly understood. To address this issue, we used RADseq to generate ∼19,000 SNPs across a worldwide collection of 37 Hv samples. Contrarily to the longstanding idea that Hv represents a genetically unstructured and cosmopolitan species, our results reveal the existence of a cryptic species complex with marked host tropism...
January 12, 2018: Molecular Plant Pathology
https://www.readbyqxmd.com/read/29324975/strong-population-bottleneck-and-repeated-demographic-expansions-of-populus-adenopoda-salicaceae-in-subtropical-china
#12
Liqiang Fan, Honglei Zheng, Richard I Milne, Lei Zhang, Kangshan Mao
Background and Aims: Glacial refugia and inter-/postglacial recolonization routes during the Quaternary of tree species in Europe and North America are well understood, but far less is known about those of tree species in subtropical eastern Asia. Thus, we have examined the phylogeographic history of Populus adenopoda (Salicaceae), one of the few poplars that naturally occur in this subtropical area. Methods: Genetic variations across the range of the species in subtropical China were surveyed using ten nuclear microsatellite loci and four chloroplast fragments (matK, trnG-psbK, psbK-psbI and ndhC-trnV)...
January 6, 2018: Annals of Botany
https://www.readbyqxmd.com/read/29322640/conserved-roles-of-osiris-genes-in-insect-development-polymorphism-and-protection
#13
Chris R Smith, Claire Morandin, Moataz Noureddine, Swati Pant
Much of the variation among insects is derived from the different ways that chitin has been molded to form rigid structures, both internal and external. In this study, we identify a highly conserved expression pattern in an insect-only gene family, the Osiris genes, that is essential for development, but also plays a significant role in phenotypic plasticity and in immunity/toxicity responses. The majority of Osiris genes exist in a highly syntenic cluster, and the cluster itself appears to have arisen very early in the evolution of insects...
January 10, 2018: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/29321589/comparative-analysis-of-low-complexity-regions-in-plasmodia
#14
S R Chaudhry, N Lwin, D Phelan, A A Escalante, F U Battistuzzi
Low complexity regions (LCRs) are a common feature shared by many genomes, but their evolutionary and functional significance remains mostly unknown. At the core of the uncertainty is a poor understanding of the mechanisms that regulate their retention in genomes, whether driven by natural selection or neutral evolution. Applying a comparative approach of LCRs to multiple strains and species is a powerful approach to identify patterns of conservation in these regions. Using this method, we investigate the evolutionary history of LCRs in the genus Plasmodium based on orthologous protein coding genes shared by 11 species and strains from primate and rodent-infecting pathogens...
January 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29321486/new-insights-on-basivenal-sclerites-using-3d-tools-and-homology-of-wing-veins-in-odonatoptera-insecta
#15
Lauriane Jacquelin, Laure Desutter-Grandcolas, Ioana Chintauan-Marquier, Renaud Boistel, Daran Zheng, Jakub Prokop, André Nel
Being implied in flight, mimetism, communication, and protection, the insect wings were crucial organs for the mega diversification of this clade. Despite several attempts, the problem of wing evolution remains unresolved because the basal parts of the veins essential for vein identification are hidden in the basivenal sclerites. The homologies between wing characters thus cannot be accurately verified, while they are of primary importance to solve long-standing problems, such as the monophyly of the Palaeoptera, viz...
January 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29320496/bayesian-inference-of-phylogenetic-networks-from-bi-allelic-genetic-markers
#16
Jiafan Zhu, Dingqiao Wen, Yun Yu, Heidi M Meudt, Luay Nakhleh
Phylogenetic networks are rooted, directed, acyclic graphs that model reticulate evolutionary histories. Recently, statistical methods were devised for inferring such networks from either gene tree estimates or the sequence alignments of multiple unlinked loci. Bi-allelic markers, most notably single nucleotide polymorphisms (SNPs) and amplified fragment length polymorphisms (AFLPs), provide a powerful source of genome-wide data. In a recent paper, a method called SNAPP was introduced for statistical inference of species trees from unlinked bi-allelic markers...
January 10, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29319812/deuterostome-genomics-lineage-specific-protein-expansions-that-enabled-chordate-muscle-evolution
#17
Jun Inoue, Noriyuki Satoh
Fish-like larvae were foundational to the chordate body plan, given the basal placement of free-living lancelets. That body plan probably made it possible for chordate ancestors to swim by beating a tail formed of notochord and bilateral paraxial muscles. In order to investigate the molecular genetic basis of the origin and evolution of paraxial muscle, we deduced the evolutionary histories of 16 contractile protein genes from paraxial muscle, based on genomic data from all five deuterostome lineages, using a newly developed orthology identification pipeline and a species tree...
January 8, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29318376/count-on-arousal-introducing-a-new-method-for-investigating-the-effects-of-emotional-valence-and-arousal-on-visual-search-performance
#18
Andras Norbert Zsido, Laszlo Bernath, Beatrix Labadi, Anita Deak
There is a large body of research, indicating that threatening stimuli with evolutionary history are prioritised in visual processing. It has been proposed that all threatening stimuli are prioritised, irrespective of evolutionary age, but it was argued that the method used to produce the results was not suitable for investigating the phenomenon. We present a new visual search task and provide evidence that it is an appropriate tool for future research. In Experiment 1, we investigated how the influence of emotional stimuli on visual search performance varies with valence (negative, positive, and neutral) and arousal (medium and high)...
January 9, 2018: Psychological Research
https://www.readbyqxmd.com/read/29317769/phylogenomic-perspective-on-the-relationships-and-evolutionary-history-of-the-major-otocephalan-lineages
#19
Wei Dai, Ming Zou, Liandong Yang, Kang Du, Weitao Chen, Yanjun Shen, Richard L Mayden, Shunping He
The phylogeny of otocephalan fishes is the subject of broad controversy based on morphological and molecular evidence. The primary unresolved issue pertaining to this lineage relates to the origin of Characiphysi, especially the paraphyly of Characiformes. The considerable uncertainty associated with this lineage has precluded a greater understanding of the origin and evolution of the clade. Herein, a phylogenomic approach was applied to resolve this debate. By analyzing 10 sets of transcriptomic data generated in this study and 12 sets of high-throughput data available in public databases, we obtained 1,110 single-copy orthologous genes (935,265 sites for analysis) from 22 actinopterygians, including 14 otocephalan fishes from six orders: Clupeiformes, Gonorynchiformes, Cypriniformes, Siluriformes, Characiformes, and Gymnotiformes...
January 9, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29315395/comparative-genomic-analyses-reveal-the-features-for-adaptation-to-nematodes-in-fungi
#20
Ruizhen Wang, Leiming Dong, Ran He, Qinghua Wang, Yuequ Chen, Liangjian Qu, Yong-An Zhang
Nematophagous (NP) fungi are ecologically important components of the soil microbiome in natural ecosystems. Esteya vermicola (Ev) has been reported as a NP fungus with a poorly understood evolutionary history and mechanism of adaptation to parasitism. Furthermore, NP fungal genomic basis of lifestyle was still unclear. We sequenced and annotated the Ev genome (34.2 Mbp) and integrated genetic makeup and evolution of pathogenic genes to investigate NP fungi. The results revealed that NP fungi had some abundant pathogenic genes corresponding to their niche...
January 5, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
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