Top 10 Biorxiv Papers Today in Evolutionary Biology


2.016 Mikeys
#1. Complex eukaryotic-like actin regulation systems from Asgard archaea
Caner Akil, Linh T Tran, Magali Orhant-Prioux, Yohendran Baskaran, Edward Manser, Laurent Blanchoin, Robert C Robinson
Asgard archaea genomes contain potential eukaryotic-like genes that provide intriguing insight for the evolution of eukaryotes. The actin polymerization/depolymerization cycle is critical for providing force and structure for a variety of processes in eukaryotes, including membrane remodelling. Here, we identify actin filament severing, capping, annealing and bundling, and monomer sequestration activities by gelsolin proteins from Thorarchaeota (Thor), which complete a eukaryote-like actin depolymerization cycle. Thor gelsolins are comprised of one or two copies of the prototypical gelsolin domain and appear to be a record of an initial pre-eukaryotic gene duplication event, since eukaryotic gelsolins are generally comprised of three to six domains. X-ray crystal structure determination of these proteins in complex with mammalian actin revealed similar interactions to the first domain of human gelsolin. Asgard two-domain, but not one-domain, gelsolins contain calcium-binding sites, which is manifested in calcium-controlled...
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BiologiaNhid: La Biologia dels arqueus està on fire! 🔥🔥 Un altre article a Biorxive parlant dels mecanismes de remodelació de la membrana...#BiologiaNHiD https://t.co/qernO4Ixrt
archaeal: RT @biorxiv_evobio: Complex eukaryotic-like actin regulation systems from Asgard archaea https://t.co/RKIXWwmmiM #biorxiv_evobio
BejaLab: RT @biorxiv_evobio: Complex eukaryotic-like actin regulation systems from Asgard archaea https://t.co/RKIXWwmmiM #biorxiv_evobio
Dey_Gautam: RT @biorxiv_evobio: Complex eukaryotic-like actin regulation systems from Asgard archaea https://t.co/RKIXWwmmiM #biorxiv_evobio
mehrshmali: RT @biorxiv_evobio: Complex eukaryotic-like actin regulation systems from Asgard archaea https://t.co/RKIXWwmmiM #biorxiv_evobio
MFSeidl: RT @biorxivpreprint: Complex eukaryotic-like actin regulation systems from Asgard archaea https://t.co/6yx02IGo0S #bioRxiv
EvolPaper: RT @biorxiv_evobio: Complex eukaryotic-like actin regulation systems from Asgard archaea https://t.co/RKIXWwmmiM #biorxiv_evobio
ElectricBiome: RT @biorxiv_evobio: Complex eukaryotic-like actin regulation systems from Asgard archaea https://t.co/RKIXWwmmiM #biorxiv_evobio
tarnotron: RT @biorxiv_evobio: Complex eukaryotic-like actin regulation systems from Asgard archaea https://t.co/RKIXWwmmiM #biorxiv_evobio
jspathmanathan: RT @biorxiv_evobio: Complex eukaryotic-like actin regulation systems from Asgard archaea https://t.co/RKIXWwmmiM #biorxiv_evobio
rcooperbaer: RT @biorxiv_evobio: Complex eukaryotic-like actin regulation systems from Asgard archaea https://t.co/RKIXWwmmiM #biorxiv_evobio
mpfrancino: RT @biorxiv_evobio: Complex eukaryotic-like actin regulation systems from Asgard archaea https://t.co/RKIXWwmmiM #biorxiv_evobio
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Authors: 7
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2.002 Mikeys
#2. Deviations from Hardy Weinberg Equilibrium at CCR5-Δ32 in Large Sequencing Data Sets
Xinzhu Wei, Rasmus Nielsen
Previous analyses of the UK Biobank (UKB) genotyping array data in the CCR5 -Δ32 locus show evidence for deviations from Hardy-Weinberg Equilibrium (HWE) and an increased mortality rate of homozygous individuals, consistent with a recessive deleterious effect of the deletion mutation. We here examine if similar deviations from HWE can be observed in the newly released UKB Whole Exome Sequencing (WES) data and in the sequencing data of the Genome Aggregation Database (gnomAD). We also examine the reliability of the genotype calls in the UKB array data. The UKB genotyping array probe targeting CCR5 -Δ32 (rs62625034) and the WES of CCR5 -Δ32 are strongly correlated ( r 2 = 0.97). This contrasts to tag SNPs of CCR5 -Δ32 in the UKB which have high missing data rates and imputation errors rates. We also show that, while different data sets are subject to different biases, both the UKB-WES and the gnomAD data have a deficiency of homozygous CCR5 -Δ32 individuals compared to the HWE expectation (combined P -value < 0.01), consistent with...
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biorxivpreprint: Deviations from Hardy Weinberg Equilibrium at CCR5-Δ32 in Large Sequencing Data Sets https://t.co/tpf4f9BK9G #bioRxiv
biorxiv_evobio: Deviations from Hardy Weinberg Equilibrium at CCR5-Δ32 in Large Sequencing Data Sets https://t.co/lHfFEZp8ug #biorxiv_evobio
richardbadge: Gonna teach with this! RT @biorxiv_evobio Deviations from Hardy Weinberg Equilibrium at CCR5-Δ32 in Large Sequencing Data Sets https://t.co/aWl4mlHJBZ #biorxiv_evobio
EvolPaper: RT @biorxiv_evobio: Deviations from Hardy Weinberg Equilibrium at CCR5-Δ32 in Large Sequencing Data Sets https://t.co/lHfFEZp8ug #biorxiv_…
ravinderkanda: RT @biorxiv_evobio: Deviations from Hardy Weinberg Equilibrium at CCR5-Δ32 in Large Sequencing Data Sets https://t.co/lHfFEZp8ug #biorxiv_…
shihuwenbo: RT @biorxiv_evobio: Deviations from Hardy Weinberg Equilibrium at CCR5-Δ32 in Large Sequencing Data Sets https://t.co/lHfFEZp8ug #biorxiv_…
chasewnelson: RT @biorxiv_evobio: Deviations from Hardy Weinberg Equilibrium at CCR5-Δ32 in Large Sequencing Data Sets https://t.co/lHfFEZp8ug #biorxiv_…
km_tsui: RT @biorxiv_evobio: Deviations from Hardy Weinberg Equilibrium at CCR5-Δ32 in Large Sequencing Data Sets https://t.co/lHfFEZp8ug #biorxiv_…
HAAANBIN: RT @biorxiv_evobio: Deviations from Hardy Weinberg Equilibrium at CCR5-Δ32 in Large Sequencing Data Sets https://t.co/lHfFEZp8ug #biorxiv_…
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1.998 Mikeys
#3. Recent hybrids recapitulate ancient hybrid outcomes
Samridhi Chaturvedi, Lauren Lucas, Alex Buerkle, James Fordyce, Matthew Forister, Chris C. Nice, Zachariah Gompert
Genomic outcomes of hybridization depend on selection and recombination in hybrids. Whether these processes have similar effects on hybrid genome composition in contemporary hybrid zones versus ancient, stabilized hybrid lineages is unknown. Here we show that patterns of introgression in a contemporary hybrid zone in Lycaeides butterflies predict patterns of ancestry in geographically adjacent, ancient hybrid populations. We find a particularly striking lack of ancestry from one of the hybridizing taxa, Lycaeides melissa, on the Z chromosome in both the ancient and contemporary hybrids. The same pattern of reduced L. melissa ancestry on the Z chromosome is seen in two other ancient hybrid lineages. More generally, we find that patterns of ancestry in ancient hybrids are remarkably predictable from contemporary hybrids, which suggests selection affects hybrid genomes in a similar way across disparate time scales and during distinct stages of speciation and species breakdown
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biorxivpreprint: Recent hybrids recapitulate ancient hybrid outcomes https://t.co/ITKD2oE56T #bioRxiv
biorxiv_evobio: Recent hybrids recapitulate ancient hybrid outcomes https://t.co/6iTIWmXviP #biorxiv_evobio
samridhichat: RT @biorxivpreprint: Recent hybrids recapitulate ancient hybrid outcomes https://t.co/ITKD2oE56T #bioRxiv
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Sample Sizes : [23]
Authors: 7
Total Words: 22710
Unqiue Words: 4901

1.998 Mikeys
#4. Open source 3D printable replacement parts for the WHO insecticide susceptibility bioassay system
Sean Tomlinson, Henrietta Carrington Yates, Ambrose Oruni, Harun Njoroge Ng'ang'a, David Weetman, Martin J Donnelly, Arjen E Van't Hof
Background: Malaria vector control and research rely heavily on monitoring mosquito populations for the development of resistance to public health insecticides. One standard method for determining susceptibility in adult mosquito populations is the World Health Organization test (WHO bioassay). The WHO bioassay kit consists of several acrylic pieces that are assembled into a unit. Parts of the kit commonly break, reducing the capacity of insectaries to carry out resistance profiling. Since there is at present only a single supplier for the test kits, replacement parts can be hard to procure in a timely fashion. Here, we present 3D printable versions for all pieces of the WHO bioassay kit. Results: Using widely available polylactic acid (PLA) filament as a printing material, we were able to design and print functional replacements for each piece of the WHO bioassay kit. We note no significant difference in mortality results obtained from PLA printed tubes and WHO acrylic tubes. Additionally, we observed no degradation of PLA in...
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Sample Sizes : [10, 11, 7, 7]
Authors: 7
Total Words: 3664
Unqiue Words: 1465

1.997 Mikeys
#5. Genetic correlations across genetically determined and developmentally plastic alternative reproductive tactics
Jessica K Abbott, Oscar Rios-Cardenas, Molly R. Morris
Alternative reproductive tactics occur when individuals of the same sex have a suite of morphological and/or behavioural traits that allow them to pursue different reproductive strategies. A common pattern is e.g. the existence of "courter" and "sneaker" tactics within males. We have previously argued that alternative reproductive tactics should be subject to genetic conflict over the phenotypic expression of traits, similar to sexual antagonism. In this process, which we called intra-locus tactical conflict, genetically determined tactics experience conflicting selection on a shared phenotypic trait, such as body size, but a positive genetic correlation between tactics in body size prevents either tactic from reaching its optimum. Recently, other authors have attempted to extend this idea to developmentally plastic alternative reproductive tactics, with mixed results. However, it is not clear whether we should expect intra-locus tactical conflict in developmentally plastic tactics or not. We have therefore run a series of...
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biorxivpreprint: Genetic correlations across genetically determined and developmentally plastic alternative reproductive tactics https://t.co/VWzNH6D3Ow #bioRxiv
biorxiv_evobio: Genetic correlations across genetically determined and developmentally plastic alternative reproductive tactics https://t.co/7nHEnBUr3u #biorxiv_evobio
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1.997 Mikeys
#6. ML-morph: A fast, accurate and general approach for automated detection and landmarking of biological structures in images
Arthur Porto, Kjetil L Voje
Morphometrics has become an indispensable component of the statistical analysis of size and shape variation in biological structures. Morphometric data has traditionally been gathered through low-throughput manual landmark annotation, which represents a significant bottleneck for morphometric-based phenomics. Here we propose a machine-learning-based high-throughput pipeline to collect high-dimensional morphometric data in images of semi rigid biological structures. The proposed framework has four main strengths. First, it allows for dense phenotyping with minimal impact on specimens. Second, it presents landmarking accuracy comparable to manual annotators, when applied to standardized datasets. Third, it performs data collection at speeds several orders of magnitude higher than manual annotators. And finally, it is of general applicability (i.e., not tied to a specific study system). State-of-the-art validation procedures show that the method achieves low error levels when applied to three morphometric datasets of increasing...
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biorxivpreprint: ML-morph: A fast, accurate and general approach for automated detection and landmarking of biological structures in images https://t.co/fozFL8MUrY #bioRxiv
biorxiv_evobio: ML-morph: A fast, accurate and general approach for automated detection and landmarking of biological structures in images https://t.co/I8v2X8Os0V #biorxiv_evobio
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1.997 Mikeys
#7. Most cancers carry a substantial deleterious load due to Hill-Robertson interference
Susanne Tilk, Christina Curtis, Dmitri Petrov, Christopher Dennis McFarland
Cancer genomes exhibit surprisingly weak signatures of negative selection1,2. This may be because tumors evolve either under very weak selective pressures (weak selection) or under conditions that prevent the elimination of many deleterious passenger mutations (poor efficacy of selection). The weak selection model argues that the majority of genes are only important for multicellular function. The poor efficacy of selection model argues, in contrast, that genome-wide linkage in cancer prevents many deleterious mutations from being removed via Hill-Robertson interference3. Since these linkage effects weaken as mutation rates decrease, we predict that cancers with lower mutational burdens should exhibit stronger signals of negative selection. Furthermore, because linkage affects driver mutations as well, low mutational burden cancers should also show stronger evidence of positive selection in driver genes. Neither pattern - in drivers or passengers - is expected under the weak selection model. We leverage the 10,000-fold variation...
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biorxivpreprint: Most cancers carry a substantial deleterious load due to Hill-Robertson interference https://t.co/OZvgE9djDi #bioRxiv
biorxiv_evobio: Most cancers carry a substantial deleterious load due to Hill-Robertson interference https://t.co/IHBIFzKsgB #biorxiv_evobio
TonyBurnetti: RT @biorxiv_evobio: Most cancers carry a substantial deleterious load due to Hill-Robertson interference https://t.co/IHBIFzKsgB #biorxiv_…
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Sample Sizes : [371, 925, 1199, 1059, 3328, 378, 2181, 614]
Authors: 4
Total Words: 16904
Unqiue Words: 3811

1.997 Mikeys
#8. Interaction between host genes and M. tuberculosis lineage can affect tuberculosis severity: evidence for co-evolution
Michael L McHenry, Jacquelaine Bartlett, Robert P Igo, Edward Wampande, Penelope Bencheck, Harriet Mayanja-Kizza, Kyle Fluegge, Noemi B Hall, Sebastien Gagneux, Sarah Tishkoff, Christian Wejse, Giorgio Sirugo, W Henry Boom, Moses Joloba, Scott M Williams, Catherine Stein
Genetic studies of both the human host and Mycobacterium tuberculosis (MTB) demonstrate independent association with tuberculosis (TB) risk. However, neither explains a large portion of disease risk or severity. Based on studies in other infectious diseases and animal models of TB, we hypothesized that the genomes of the two interact to modulate risk of developing active TB or increasing the severity of disease, when present. We examined this hypothesis in our TB household contact study in Kampala, Uganda, in which there were 3 MTB lineages of which L4-Ugandan (L4.6) is the most recent. TB severity, measured using the Bandim TBscore, was modeled as a function of host SNP genotype, MTB lineage, and their interaction, within two independent cohorts of TB cases, N=113 and 122. No association was found between lineage and severity, but association between multiple polymorphisms in IL12B and TBscore was replicated in two independent cohorts (most significant rs3212227, combined p=0.0006), supporting previous associations of IL12B with...
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biorxivpreprint: Interaction between host genes and M. tuberculosis lineage can affect tuberculosis severity: evidence for co-evolution https://t.co/avL0It7JXQ #bioRxiv
biorxiv_evobio: Interaction between host genes and M. tuberculosis lineage can affect tuberculosis severity: evidence for co-evolution https://t.co/6Xopm4GC2t #biorxiv_evobio
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Authors: 16
Total Words: 0
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1.997 Mikeys
#9. A Bayesian implementation of the multispecies coalescent model with introgression for comparative genomic analysis
Thomas Flouris, Xiyun Jiao, Bruce Rannala, Ziheng Yang
Recent analyses suggest that cross-species gene flow or introgression is common in nature, especially during species divergences. Genomic sequence data can be used to infer introgression events and to estimate the timing and intensity of introgression, providing an important means to advance our understanding of the role of gene flow in speciation. Here we implement the multispecies-coalescent-with-introgression (MSci) model, an extension of the multispecies-coalescent (MSC) model to incorporate introgression, in our Bayesian Markov chain Monte Carlo (MCMC) program BPP. The MSci model accommodates deep coalescence (or incomplete lineage sorting) and introgression and provides a natural framework for inference using genomic sequence data. Computer simulation confirms the good statistical properties of the method, although hundreds or thousands of loci are typically needed to estimate introgression probabilities reliably. Re-analysis of datasets from the purple cone spruce confirms the hypothesis of homoploid hybrid speciation. We...
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biorxivpreprint: A Bayesian implementation of the multispecies coalescent model with introgression for comparative genomic analysis https://t.co/ASQDPbnas9 #bioRxiv
biorxiv_evobio: A Bayesian implementation of the multispecies coalescent model with introgression for comparative genomic analysis https://t.co/sEsAajFdti #biorxiv_evobio
razoralign: A Bayesian implementation of the multispecies coalescent model with introgression for comparative genomic analysis https://t.co/uJPCd3GvAd https://t.co/5DSB42qGCS
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1.997 Mikeys
#10. The conserved regulatory basis of mRNA contributions to the early Drosophila embryo differs between the maternal and zygotic genomes
Charles S Omura, Susan E Lott
The gene products that drive early development are critical for setting up developmental trajectories in all animals. The earliest stages of development are fueled by maternally provided mRNAs until the zygote can take over transcription of its own genome. In early development, both maternally deposited and zygotically transcribed gene products have been well characterized in model systems. Previously, we demonstrated that across the genus Drosophila, maternal and zygotic mRNAs are largely conserved but also showed a surprising amount of change across species, with more differences evolving at the zygotic stage than the maternal stage. In this study, we use comparative methods to elucidate the regulatory mechanisms underlying maternal deposition and zygotic transcription across species. Through motif analysis, we discovered considerable conservation of regulatory mechanisms associated with maternal transcription, as compared to zygotic transcription. We also found that the regulatory mechanisms active in the two genomes, maternal...
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