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Genome Biology and Evolution

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https://www.readbyqxmd.com/read/29045655/determinants-of-the-efficacy-of-natural-selection-on-coding-and-noncoding-variability-in-two-passerine-species
#1
Pádraic Corcoran, Toni I Gossmann, Henry J Barton, Jon Slate, Kai Zeng
Population genetic theory predicts that selection should be more effective when the effective population size (Ne) is larger, and that the efficacy of selection should correlate positively with recombination rate. Here, we analysed the genomes of 10 great tits and 10 zebra finches. Nucleotide diversity at 4-fold degenerate sites indicates that zebra finches have a 2.83-fold larger Ne. We obtained clear evidence that purifying selection is more effective in zebra finches. The proportion of substitutions at 0-fold degenerate sites fixed by positive selection (α) is high in both species (great tit 48%; zebra finch 64%) and is significantly higher in zebra finches...
October 17, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29045639/a-new-perspective-on-polyploid-fragaria-strawberry-genome-composition-based-on-large-scale-multi-locus-phylogenetic-analysis
#2
Yilong Yang, Thomas M Davis
The subgenomic compositions of the octoploid (2n=8x=56) strawberry (Fragaria) species, including the economically important cultivated species Fragaria x ananassa, have been a topic of long-standing interest. Phylogenomic approaches utilizing next generation sequencing (NGS) technologies offer a new window into species relationships and the subgenomic compositions of polyploids. We have conducted a large scale phylogenetic analyses of Fragaria (strawberry) species using the Fluidigm Access Array system and 454 sequencing platform...
October 16, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29045601/genomic-changes-associated-with-reproductive-and-migratory-ecotypes-in-sockeye-salmon-oncorhynchus-nerka
#3
Andrew J Veale, Michael A Russello
Mechanisms underlying adaptive evolution can best be explored using paired populations displaying similar phenotypic divergence, illuminating the genomic changes associated with specific life history traits. Here we used paired migratory [anadromous vs. resident (kokanee)] and reproductive [shore- vs. stream-spawning] ecotypes of sockeye salmon (Oncorhynchus nerka) sampled from seven lakes and two rivers spanning three catchments (Columbia, Fraser, and Skeena) in British Columbia, Canada to investigate the patterns and processes underlying their divergence...
October 13, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29040546/variation-and-functional-impact-of-neanderthal-ancestry-in-western-asia
#4
Recep Ozgur Taskent, Duha Alioglu, Evrim Fer, Handan Melike Donertas, Mehmet Somel, Omer Gokcumen
Neanderthals contributed genetic material to modern humans via multiple admixture events. Initial admixture events presumably occurred in Western Asia shortly after humans migrated out-of-Africa. Despite being a focal point of admixture, earlier studies indicate lower Neanderthal introgression rates in some Western Asian populations as compared to other Eurasian populations. To better understand the genome-wide and phenotypic impact of Neanderthal introgression in the region, we sequenced whole genomes of 10 present-day Europeans, Africans, and the Western Asian Druze at high depth, and analyzed available whole genome data from various other populations, including 16 genomes from present-day Turkey...
October 13, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29036566/the-role-of-alternative-splicing-and-differential-gene-expression-in-cichlid-adaptive-radiation
#5
Pooja Singh, Christine Börger, Heather More, Christian Sturmbauer
Species diverge eco-morphologically through the continuous action of natural selection on functionally important structures, producing alternative adaptive morphologies. In cichlid fishes, the oral and pharyngeal jaws are such key structures. Adaptive variation in jaw morphology contributes to trophic specialisation, which is hypothesised to fuel their rapid speciation in the East African Great Lakes. Much is known about the genes involved in cichlid jaw and craniofacial development. However, it is still unclear what salient sources of variation gave rise to trophic-niche specialisation, facilitating adaptive radiation...
September 27, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29036316/the-role-of-small-rna-based-epigenetic-silencing-for-purifying-selection-on-transposable-elements-in-capsella-grandiflora
#6
Robert Horvath, Tanja Slotte
To avoid negative effects of transposable element (TE) proliferation, plants epigenetically silence TEs using a number of mechanisms, including RNA-directed DNA methylation. These epigenetic modifications can extend outside the boundaries of TE insertions and lead to silencing of nearby genes, resulting in a trade-off between TE silencing and interference with nearby gene regulation. Therefore, purifying selection is expected to remove silenced TE insertions near genes more efficiently and prevent their accumulation within a population...
September 27, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29036592/gain-and-loss-of-small-rna-classes-characterization-of-small-rnas-in-the-parasitic-nematode-family-strongyloididae
#7
Anja Holz, Adrian Streit
The nematode family Strongyloididae is of particular interest because it contains important parasites of medical and veterinary relevance. In addition, species of this family can form parasitic and free-living generations and it also occupies an interesting phylogenetic position within the nematodes. Nematodes differ in several ways from other taxa with respect to their small non-coding RNAs. Recent comparative studies revealed that there is also considerable variability within the nematodes. However, no Strongyloididae species or close relative was included in these studies...
September 25, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29036491/transcription-associated-compositional-skews-in-drosophila-genes
#8
Juraj Bergman, Andrea J Betancourt, Claus Vogl
In many organisms, local deviations from Chargaff's second parity rule are observed around replication and transcription start sites and within intron sequences. Here, we use expression data as well as a whole-genome dataset of nearly 200 haplotypes to investigate such compositional skews in Drosophila melanogaster genes. We find a positive correlation between compositional skew and gene expression, comparable in strength to similar correlations between expression levels and genome-wide sequence features. This correlation is relatively stronger for germline, compared to somatic expression, consistent with the process of transcription-associated mutation bias...
September 25, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29036466/insights-into-epigenome-evolution-from-animal-and-plant-methylomes
#9
Soojin V Yi
Evolutionary studies of DNA methylation begin to provide insights into the underlying forces governing the variation of genomic DNA methylation across different species. Comparisons of gross levels of DNA methylation between distantly related species indicate that the size of the genome and the level of genomic DNA methylation are positively correlated. In plant genomes, this can be reliably explained by the contents of repetitive sequences, while the underlying driver of this correlation is less clear in animal genomes...
September 25, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29036401/the-all-rounder-sodalis-a-new-bacteriome-associated-endosymbiont-of-the-lygaeoid-bug-henestaris-halophilus-heteroptera-henestarinae-and-a-critical-examination-of-its-evolution
#10
Diego Santos-Garcia, Francisco J Silva, Shai Morin, Konrad Dettner, Stefan Martin Kuechler
Hemipteran insects are well-known in their ability to establish symbiotic relationships with bacteria. Among them, heteropteran insects present an array of symbiotic systems, ranging from the most common gut crypt symbiosis to the more restricted bacteriome-associated endosymbiosis, which have only been detected in members of the superfamily Lygaeoidea and the family Cimicidae so far. Genomic data of heteropteran endosymbionts are scarce and have merely been analyzed from the Wolbachia endosymbiont in bed bug and a few gut crypt-associated symbionts in pentatomoid bugs...
September 25, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29036290/comparative-genomics-of-apomictic-root-knot-nematodes-hybridization-ploidy-and-dynamic-genome-change
#11
Amir Szitenberg, Laura Salazar-Jaramillo, Vivian C Blok, Dominik R Laetsch, Soumi Joseph, Valerie M Williamson, Mark L Blaxter, David H Lunt
The Root-Knot Nematodes (RKN; genus Meloidogyne) are important plant parasites causing substantial agricultural losses. The Meloidogyne incognita group (MIG) of species, most of which are obligatory apomicts (mitotic parthenogens), are extremely polyphagous and important problems for global agriculture. While understanding the genomic basis for their variable success on different crops could benefit future agriculture, analyses of their genomes are challenging due to complex evolutionary histories that may incorporate hybridization, ploidy changes, and chromosomal fragmentation...
September 25, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29036288/strategies-for-partitioning-clock-models-in-phylogenomic-dating-application-to-the-angiosperm-evolutionary-timescale
#12
Charles S P Foster, Simon Y W Ho
Evolutionary timescales can be inferred from molecular sequence data using a Bayesian phylogenetic approach. In these methods, the molecular clock is often calibrated using fossil data. The uncertainty in these fossil calibrations is important because it determines the limiting posterior distribution for divergence-time estimates as the sequence length tends to infinity. Here we investigate how the accuracy and precision of Bayesian divergence-time estimates improve with the increased clock-partitioning of genome-scale data into clock-subsets...
September 25, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28985302/net-evolutionary-loss-of-residue-polarity-in-drosophilid-protein-cores-indicates-ongoing-optimization-of-amino-acid-composition
#13
Lev Y Yampolsky, Yuri I Wolf, Michael A Bouzinier
Amino acid frequencies in proteins may not be at equilibrium. We consider two possible explanations for the non-zero net residue fluxes in drosophilid proteins. First, protein interiors may have a suboptimal residue composition and be under a selective pressure favoring stability, i.e., leading to the loss of polar (and the gain of large) amino acids. One would then expect stronger net fluxes on the protein interior than at the exposed sites. Alternatively, if most of the polarity loss occurs at the exposed sites and the selective constraint on amino acid composition at such sites decreases over time, net loss of polarity may be neutral and caused by disproportionally high occurrence of polar residues at exposed, least constrained sites...
September 18, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28985297/gene-regulatory-enhancers-with-evolutionarily-conserved-activity-are-more-pleiotropic-than-those-with-species-specific-activity
#14
Alexandra Fish, Ling Chen, John A Capra
Studies of regulatory activity and gene expression have revealed an intriguing dichotomy: there is substantial turnover in the regulatory activity of orthologous sequences between species; however, the expression level of orthologous genes is largely conserved. Understanding how distal regulatory elements, e.g., enhancers, evolve and function is critical, as alterations in gene expression levels can drive the development of both complex disease and functional divergence between species. In this study, we investigated determinants of the conservation of regulatory enhancer activity for orthologous sequences across mammalian evolution...
September 18, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28985291/mobile-genetic-elements-and-evolution-of-crispr-cas-systems-all-the-way-there-and-back
#15
Eugene V Koonin, Kira S Makarova
The CRISPR-Cas systems of bacterial and archaeal adaptive immunity show multifaceted evolutionary relationships with at least five classes of mobile genetic elements (MGE). First, the adaptation module of CRISPR-Cas that is responsible for the formation of the immune memory apparently evolved from a Casposon, a self-synthesizing transposon that employs the Cas1 protein as the integrase and might have brought additional cas genes to the emerging immunity loci. Second, a large subset of type III CRISPR-Cas systems recruited a reverse transcriptase from a Group II intron, providing for spacer acquisition from RNA...
September 18, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28985307/sequence-based-analysis-of-thermal-adaptation-and-protein-energy-landscapes-in-an-invasive-blue-mussel-mytilus-galloprovincialis
#16
Norah P Saarman, Kord M Kober, W Brian Simison, Grant H Pogson
Adaptive responses to thermal stress in poikilotherms plays an important role in determining competitive ability and species distributions. Amino acid substitutions that affect protein stability and modify the thermal optima of orthologous proteins may be particularly important in this context. Here, we examine a set of 2,770 protein-coding genes to determine if proteins in a highly invasive heat tolerant blue mussel (Mytilus galloprovincialis) contain signals of adaptive increases in protein stability relative to orthologs in a more cold-tolerant M...
September 14, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28985367/the-novel-evolution-of-the-sperm-whale-genome
#17
Wesley C Warren, Lukas Kuderna, Alana Alexander, Julian Catchen, José G Pérez-Silva, Carlos López-Otín, Víctor Quesada, Patrick Minx, Chad Tomlinson, Michael J Montague, Fabiana H G Farias, Ronald B Walter, Tomas Marques-Bonet, Travis Glenn, Troy J Kieran, Sandra S Wise, John Pierce Wise, Robert M Waterhouse, John Pierce Wise
The sperm whale, made famous by Moby Dick, is one of the most fascinating of all ocean-dwelling species given their unique life history, novel physiological adaptations to hunting squid at extreme ocean depths, and their position as one of the earliest branching toothed whales (Odontoceti). We assembled the sperm whale (Physeter macrocephalus) genome and resequenced individuals from multiple ocean basins to identify new candidate genes for adaptation to an aquatic environment and infer demographic history. Genes crucial for skin integrity appeared to be particularly important in both the sperm whale and other cetaceans...
September 13, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28985292/extreme-deviations-from-expected-evolutionary-rates-in-archaeal-protein-families
#18
Celine Petitjean, Kira S Makarova, Yuri I Wolf, Eugene V Koonin
Origin of new biological functions is a complex phenomenon ranging from single-nucleotide substitutions to the gain of new genes via horizontal gene transfer or duplication. Neofunctionalization and subfunctionalization of proteins is often attributed to the emergence of paralogs that are subject to relaxed purifying selection or positive selection and thus evolve at accelerated rates. Such phenomena potentially could be detected as anomalies in the phylogenies of the respective gene families. We developed a computational pipeline to search for such anomalies in 1834 orthologous clusters of archaeal genes (arCOGs), focusing on lineage-specific subfamilies that significantly deviate from the expected rate of evolution...
September 13, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28985306/plastome-evolution-in-the-sole-hemiparasitic-genus-laurel-dodder-cassytha-and-insights-into-the-plastid-phylogenomics-of-lauraceae
#19
Chung-Shien Wu, Ting-Jen Wang, Chia-Wen Wu, Ya-Nan Wang, Shu-Miaw Chaw
To date, little is known about the evolution of plastid genomes (plastomes) in Lauraceae. As one of the top five largest families in tropical forests, the Lauraceae contain many species that are important ecologically and economically. Lauraceous species also provide wonderful materials to study the evolutionary trajectory in response to parasitism because they contain both non-parasitic and parasitic species. This study compared the plastomes of nine Lauraceous species, including the sole hemiparasitic and herbaceous genus Cassytha (laurel dodder; here represented by Cas...
September 6, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28985301/the-trouble-with-meam2-implications-of-pseudogenes-on-species-delimitation-in-the-globally-invasive-bemisia-tabaci-hemiptera-aleyrodidae-cryptic-species-complex
#20
W T Tay, S Elfekih, L N Court, K H J Gordon, H Delatte, P J De Barro
Molecular species identification using sub-optimal PCR primers can over-estimate species diversity due to co-amplification of nuclear mitochondrial (NUMT) DNA/pseudogenes. For the agriculturally important whitefly Bemisia tabaci cryptic pest species complex, species identification depends primarily on characterisation of the mitochondrial DNA cytochrome oxidase I (mtDNA COI) gene. The lack of robust PCR primers for the mtDNA COI gene can undermine correct species identification which in turn compromises management strategies...
September 6, 2017: Genome Biology and Evolution
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