Orthologs diverge after speciation events and paralogs after gene duplication. It is thus expected that orthologs would tend to keep their functions, while paralogs could be a source of new functions. Because protein functional divergence follows from non-synonymous substitutions, we performed an analysis based on the ratio of non-synonymous to synonymous substitutions (dN/dS) as proxy for functional divergence. We used four working definitions of orthology, including reciprocal best hits (RBH),...
Sun Jun 21, 2020 03:00
Background: Short tandem repeats (STRs) contribute significantly to de novo mutagenesis, driving phenotypic diversity and genetic disease. Although highly diverse, their repetitive sequences induce DNA polymerase slippage and stalling, leading to length and sequence variation. However, current studies of DNA synthesis through STRs are restricted to a handful of selected sequences, limiting our broader understanding of their evolutionary behaviour and hampering the characterisation of the determinants...
Sat Jun 20, 2020 03:00
The rooting of the SARS-CoV-2 phylogeny is important for understanding the origin and early spread of the virus. Previously published phylogenies have used different rootings that do not always provide consistent results. We use several different strategies for rooting the SARS-CoV-2 tree and provide measures of statistical uncertainty for all methods. We show that methods based on the molecular clock tend to place the root in the B clade, while methods based on outgroup rooting tend to place the...
Sat Jun 20, 2020 03:00
Lateral DNA transfer plays an important role in the evolution of genetic diversity in prokaryotes. DNA acquisition via transformation involves the uptake of DNA from the environment. The ability of recipient cells to actively transport DNA into the cytoplasm - termed natural competence - depends on the presence of type IV pili and competence proteins. Natural competence has been described in cyanobacteria for several organisms including unicellular and filamentous species. However, the presence of...
Sat Jun 20, 2020 03:00
Learning about the roles that duplicate genes play in the origins of novel phenotypes requires an understanding of how their functions evolve. To date, only one method--CDROM--has been developed with this goal in mind. In particular, CDROM employs gene expression distances as proxies for functional divergence, and then classifies the evolutionary mechanisms retaining duplicate genes from comparisons of these distances in a decision tree framework. However, CDROM does not account for stochastic shifts...
Sat Jun 20, 2020 03:00
Drug-resistant parasites threaten livestock production. Breeding more resistant hosts could be a sustainable control strategy. Environmental variation may however alter the expression of genetic potential and directional selection toward host resistance could initiate an arms race between the host and its parasites. We created sheep lines with high or low resistance to Haemonchus contortus. We first exposed both lines to chronic stress or to the infection by another parasite Trichostrongylus colubriformis,...
Sat Jun 20, 2020 03:00
Understanding rapid adaptation requires quantifying natural selection on traits and elucidating the genotype-phenotype relationship for those traits. However, recent studies have often failed to predict the direction of adaptive allelic variation in natural populations from laboratory studies. Here, we test for genomic signatures of genetic correlations to illustrate how multifarious, correlational selection may drive counterintuitive patterns of population divergence in the apple maggot fly, Rhagoletis...
Sat Jun 20, 2020 03:00
In the last 240,000 years, males of the Drosophila simulans species clade have evolved striking differences in the morphology of their epandrial posterior lobes and claspers (surstyli). These changes have most likely been driven by sexual selection and mapping studies indicate a highly polygenic and generally additive genetic basis. However, we have limited understanding of the gene regulatory networks that control the development of genital structures and how they evolved to result in this rapid...
Sat Jun 20, 2020 03:00
Body size has a fundamental impact on the ecology and physiology of animals. Large size, for instance, is often associated with increased fecundity and reproductive success. A persistent correlation between body size and individual longevity is also observed across the animal world, although this relationship proved difficult to understand due to the inseparability of body size from growth rate and the widespread collinear relationship between body size with other life history traits. Here, we used...
Sat Jun 20, 2020 03:00
Tube anemones, or cerianthids, are a phylogenetically informative group of cnidarians with complex life histories, including a pelagic larval stage and tube-dwelling adult stage, both known to utilize venom in stinging-cell rich tentacles. Cnidarians are an entirely venomous group that utilize their proteinaceous-dominated toxins to capture prey and defend against predators, in addition to several other ecological functions, including intraspecific interactions. At present there are no studies describing...
Sat Jun 20, 2020 03:00
Pathogens experience selection at multiple scales, given the need to transmit between hosts and replicate within them. This presents the challenge of cross-scale selective conflict when adaptations to one scale compromise fitness at another, such as mutations that improve transmissibility but make individuals less competitive within hosts. Selection operates differently at these scales, with tight transmission bottlenecks subjecting pathogen populations to genetic drift, and large population sizes...
Sat Jun 20, 2020 03:00
Hybridization may often be an important source of adaptive variation, but the extent and long-term impacts of introgression have seldom been evaluated in the phylogenetic context of a radiation. Hares (Lepus) represent a widespread mammalian radiation of 32 extant species characterized by striking ecological adaptations and recurrent admixture. To understand the relevance of introgressive hybridization during the diversification of Lepus, we analyzed whole exome sequences (61.7 Mb) from 15 species...
Sat Jun 20, 2020 03:00
The genomes of non-bilaterian metazoans are key to understanding the molecular basis of early animal evolution. However, a full comprehension of how animal-specific traits such as nervous systems arose is hindered by the scarcity and fragmented nature of genomes from key taxa, such as Porifera. Ephydatia muelleri is a freshwater sponge found across the northern hemisphere. Here we present its 326 Mb genome, assembled to high contiguity (N50: 9.88 Mb) with 23 chromosomes on 24 scaffolds. Our analyses...
Sat Jun 20, 2020 03:00
The Extended Evolutionary Synthesis invokes a role for development in shaping adaptive evolution, which in population genetics terms corresponds to mutation-biased adaptation. Critics have claimed that clonal interference makes mutation-biased adaptation rare. We consider the behavior of two simultaneously adapting traits, one with larger mutation rate U, the other with larger selection coefficient s, using asexual traveling wave models. We find that adaptation is dominated by whichever trait has...
Fri Jun 19, 2020 03:00
Satellite viruses are small, RNA-based hyper-parasites which obligately require helper viruses to transmit within and between hosts. The evolutionary pathways through which satellites spread among host species are largely unknown but define their potential as emerging pathogens. Here using metagenomic and field studies of bats, we show that deltaviruses, a medically important group of animal infecting satellites, are capable of transmitting between host species. Among 44 bat genera from 11 countries...
Fri Jun 19, 2020 03:00
The carpel is the definitive structure of angiosperms, the origin of carpel is of great significance to the phylogenetic origin of angiosperms. Traditional view was that angiosperm carpels were derived from structures similar to macrosporophylls of pteridosperms or Bennettitales, which bear ovules on the surfaces of foliar organs. In contrast, other views indicate that carpels are originated from the foliar appendage enclosing the ovule-bearing axis. One of the key differences between these two conflicting...
Fri Jun 19, 2020 03:00
The hand of molecular mimicry in shaping SARS-CoV-2 evolution and immune evasion remains to be deciphered. Here, we identify 33 distinct 8-mer/9-mer peptides that are identical between SARS-CoV-2 and human proteomes, including 20 novel peptides not observed in any previous human coronavirus (HCoV) strains. Four of these mimicked 8-mers/9-mers map onto HLA-B*40:01, HLA-B*40:02, and HLA-B*35:01 binding peptides from human PAM, ANXA7, PGD, and ALOX5AP proteins. This striking mimicry of multiple human...
Fri Jun 19, 2020 03:00
Genome size of plants has long piqued the interest of researchers due to the vast differences among organisms. However, the mechanisms that drive size differences have yet to be fully understood. Two important contributing factors to genome size are expansions of repetitive elements, such as transposable elements (TEs), and whole-genome duplications (WGD). Although studies have found correlations between genome size and both TE abundance and polyploidy, these studies typically test for these patterns...
Fri Jun 19, 2020 03:00
Although homologous recombination is accepted to be common in bacteria, so far it has been challenging to accurately quantify its impact on genome evolution within bacterial species. We here introduce methods that use the statistics of single-nucleotide polymorphism (SNP) splits in the core genome alignment of a set of strains to show that, for many bacterial species, recombination dominates genome evolution. Each genomic locus has been overwritten so many times by recombination that it is impossible...
Fri Jun 19, 2020 03:00
Factors that influence the distribution, abundance, and diversification of species can simultaneously affect multiple evolutionary lineages within or across communities. These include changes to the environment or inter-specific ecological interactions that cause ranges of multiple species to contract, expand, or fragment. Such processes predict temporally clustered evolutionary events across species, such as synchronous population divergences and/or changes in population size. There have been a...
Fri Jun 19, 2020 03:00
The Bayesian framework offers a flexible language for the consistent modular assembly of statistical models used by both minds and machines. Another algorithmic domain capable of adaptation in potentially high-dimensional and uncertain environments is Darwinian evolution. The equivalence of their fundamental dynamical equations, replicator dynamics and Bayesian update, hints at a deeper algorithmic analogy. Here we show, based on a unified mathematical discussion of evolutionary dynamics and statistical...
Fri Jun 19, 2020 03:00
Since the start of the COVID-19 pandemic, an unprecedented number of genomic sequences of the causative virus (SARS-CoV-2) have been publicly released. The resulting volume of available genetic data presents a unique opportunity to gain real-time insights into the pandemic, but also a daunting computational hurdle if analysed with gold-standard phylogeographic methods. We here describe and apply an analytical pipeline that is a compromise between fast and rigorous analytical steps. As a proof of...
Fri Jun 19, 2020 03:00
Dietary restriction (DR), limiting calories or specific nutrients, extends lifespan across diverse taxa. This lifespan extension has been explained as diet-mediated changes in the trade-off between lifespan and reproduction, with survival favoured with scarce resources. Another evolutionary hypothesis suggests the selective benefit of the response is the maintenance of reproduction. This hypothesis predicts that lifespan extension is a side effect of benign laboratory conditions, where DR individuals...
Fri Jun 19, 2020 03:00
AO_SCPLOWBSTRACTC_SCPLOWGenome sequence data are routinely being used to infer phylogenetic history within and between closely related diploid species, but few tree inference methods are specifically tailored to diploid genotype data. Here we re-examine the method of "polymorphism parsimony" (Inger 1967; Farris 1978; Felsenstein 1979), originally introduced to study morphological characters and chromosome inversion polymorphisms, to evaluate its utility for unphased diploid genotype data in large...
Sun Jun 21, 2020 03:00
Levels of sex differences for human body size and shape phenotypes are hypothesized to have been reduced following the agricultural transition, as an evolutionary response to changing socioeconomic behaviors including relatively more equal divisions of labor and the adoption of new technologies. Here we apply a multi-step approach to study the recent evolutionary history of genetic variants associated with five sexually differentiated human phenotypes: height, body mass, hip circumference, body fat...
Sun Jun 21, 2020 03:00
Whiteflies (Hemiptera: Sternorrhyncha: Aleyrodidae) are a superfamily of small phloem-feeding insects. Their taxonomy is currently based on the morphology of nymphal stages that display phenotypic plasticity, which produces inconsistencies. To overcome this limitation, we developed a new phylogenetic framework that targets five genes of Candidatus Portiera aleyrodidarum, the primary endosymbiont of whiteflies. Portiera lineages have been co-diverging with whiteflies since their origin and therefore...
Sun Jun 21, 2020 03:00
O_LIMetabarcoding of Metazoa using mitochondrial genes is confounded by the co-amplification of mitochondrial pseudogenes (NUMTs). Current denoising protocols have been designed to remove PCR and sequencing artefacts, but pseudogenes are not usually recognised by these procedures. Authentic mitochondrial amplicon sequence variants (ASVs), which represent the majority of reads, can be distinguished from PCR-derived errors, sequencing errors and NUMTs (non-authentic ASVs) due to their lower abundances....
Sun Jun 21, 2020 03:00
Metabolism across all known living systems combines two key features. First, all of the molecules that are required are either available in the environment or can be built up from available resources via other reactions within the system. Second, the reactions proceed in a fast and synchronised fashion via catalysts that are also produced within the system. Building on early work by Stuart Kauffman, a precise mathematical model for describing such self-sustaining autocatalytic systems (RAF theory)...
Thu Jun 18, 2020 03:00
The Ichneumonoidea (Ichneumonidae and Braconidae) is an incredibly diverse superfamily of parasitoid wasps that includes species that produce virus-like entities in their reproductive tracts to promote successful parasitism of host insects. Research on these entities has traditionally focused upon two viral genera Bracovirus (in Braconidae) and Ichnovirus (in Ichneumonidae). These viruses are produced using genes known collectively as endogenous viral elements (EVEs) that represent historical, now...
Sun Jun 21, 2020 03:00
The study of biogeographic barriers have been instrumental in understanding the evolution and distribution of taxa. Now with the increased availability of empirical datasets, it is possible to infer emergent patterns from communities by synthesizing how barriers filter and structure populations across species. We assemble phylogeographic data for a barrier and perform spatially-explicit simulations to quantify temporal and spatial patterns of divergence, the influence of species traits on these patterns,...
Thu Jun 18, 2020 03:00
Pathogens experience selection at multiple scales, given the need to transmit between hosts and replicate within them. This presents the challenge of cross-scale selective conflict when adaptations to one scale compromise fitness at another, such as mutations that improve transmissibility but make individuals less competitive within hosts. Selection operates differently at these scales, with tight transmission bottlenecks subjecting pathogen populations to genetic drift, and large population sizes...
Thu Jun 18, 2020 03:00
Ichneumonoidea is one of the most diverse lineages of animals on the planet with more than 48,000 described species and many more undescribed. Parasitoid wasps of this superfamily are beneficial insects that attack and kill other arthropods and are important for understanding diversification and the evolution of life history strategies related to parasitoidism. Further, some lineages of parasitoids within Ichneumonoidea have acquired endogenous virus elements (EVEs) that are permanently a part of...
Sun Jun 21, 2020 03:00
Analyst, 2020, Accepted ManuscriptDOI: 10.1039/D0AN00655F, PaperHyo Yong Kim, Chang Yeol Lee, Hansol Kim, Ki Soo Park, Hyun Gyu ParkWe herein describe a portable glucose meter (PGM)-utilized label-free and washing-free method for the facile determination of telomerase activity, which relies on the kinase-catalyzed cascade enzymatic reaction (KCER) that transduces...The content of this RSS Feed (c) The Royal Society of Chemistry
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Analyst, 2020, Accepted ManuscriptDOI: 10.1039/D0AN00999G, PaperHuanyu Chi, Concheng Wang, Zhien Wang, Hongni Zhu, Vince St. Dollente Mesias, Xin Dai, Qing Chen, Wei Liu, Jinqing HuangSurface-enhanced Raman spectroscopy (SERS) enables pesticide detection at the point-of-need, but its practical application is limited by the expensive and disposable SERS substrates. Here, we report a reusable nanoporous silver...The content of this RSS Feed (c) The Royal Society of Chemistry
Fri Jun 19, 2020 02:00
Related Articles Pre-treatment intravoxel incoherent motion diffusion-weighted imaging predicts treatment outcome in nasopharyngeal carcinoma. Eur J Radiol. 2020 Jun 11;129:109127 Authors: Qamar S, King AD, Ai QH, So TY, Mo FKF, Chen W, Poon DMC, Tong M, Ma BB, Hui EP, Yeung DK, Wang YX, Yuan J Abstract PURPOSE: To evaluate whether pre-treatment intravoxel incoherent motion diffusion-weighted imaging (IVIM-DWI) can predict treatment outcome...
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British Journal of Cancer, Published online: 22 June 2020; doi:10.1038/s41416-020-0941-4Serial circulating tumour DNA analysis for locally advanced rectal cancer treated with preoperative therapy: prediction of pathological response and postoperative recurrence
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British Journal of Cancer, Published online: 22 June 2020; doi:10.1038/s41416-020-0937-0Machine learning-based lifetime breast cancer risk reclassification compared with the BOADICEA model: impact on screening recommendations
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British Journal of Cancer, Published online: 22 June 2020; doi:10.1038/s41416-020-0932-5Cytochrome P450 1B1 polymorphism drives cancer cell stemness and patient outcome in head-and-neck carcinoma
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