Top 10 Biorxiv Papers Today in Evolutionary Biology


2.009 Mikeys
#1. Survival of adult barn owls is linked to corticosterone levels
Paul Béziers, Fränzi Korner, Lukas Jenni, Alexandre Roulin, Bettina Almasi
Glucocorticoid hormones, such as corticosterone, are fundamental in the translation of external stimuli into physiological adjustments that promote the survival of an organism in face of changes in its environment. At baseline levels, corticosterone is crucial in regulating daily life metabolism and energy expenditure, whereas the acute corticosterone response promotes short-term physiological and behavioral responses to unpredictable environmental challenges. Given their different physiological effects and their role in mediating fitness components, it is still unclear whether and how inter-individual variation in baseline corticosterone levels and acute stress-response levels can affect the survival of organisms. We used 13 years of capture-recapture and dead recovery data combined with 11 years of corticosterone measurements taken on breeding barn owls (Tyto alba) to investigate how survival probability varies in relation to baseline and stress-induced corticosterone levels. Our study shows that males with a higher level of...
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biorxivpreprint: Survival of adult barn owls is linked to corticosterone levels https://t.co/4qERHbARdh #bioRxiv
biorxiv_evobio: Survival of adult barn owls is linked to corticosterone levels https://t.co/bik9v1q1n1 #biorxiv_evobio
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Sample Sizes : None.
Authors: 5
Total Words: 9795
Unqiue Words: 3050

2.008 Mikeys
#2. Modelling the evolution of viral oncogenesis
Carmen Lia Murall, Samuel Alizon
Most human oncogenic viruses share several characteristics, such as being DNA viruses, having long (co)evolutionary histories with their hosts and causing either latent or chronic infections. They can reach high prevalences while causing relatively low case mortality, which makes them quite fit according to virulence evolution theory. After analysing the life-histories of DNA oncoviruses, we use a mathematical modelling approach to investigate how the virus life cycle may generate selective pressures favouring or acting against oncogenesis at the within-host or at the between-host level. In particular, we focus on two oncoprotein activities, namely extending cell life expectancy and increasing cell proliferation rate. These have immediate benefits (increasing viral population size) but can be associated with fitness costs at the epidemiological level (increasing recovery rate or risk of cancer) thus creating evolutionary trade-offs. We interpret the results of our nested model in the light of the biological features and identify...
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cl_murall: Our latest thoughts on the evolution of viral oncogenesis are up on Biorxiv. We developed a theoretical approach for comparing across human oncoviruses (various DNA and retro-viruses). Let's figure out why some are more virulent than others, shall we? https://t.co/PrEFrZaLvT
DrJDennehy: RT @biorxiv_evobio: Modelling the evolution of viral oncogenesis https://t.co/pURF06OmeW #biorxiv_evobio
coevoeco: RT @biorxiv_evobio: Modelling the evolution of viral oncogenesis https://t.co/pURF06OmeW #biorxiv_evobio
RemakeSystems: RT @biorxiv_evobio: Modelling the evolution of viral oncogenesis https://t.co/pURF06OmeW #biorxiv_evobio
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Sample Sizes : None.
Authors: 2
Total Words: 7041
Unqiue Words: 2211

2.005 Mikeys
#3. Comparative analyses of chromatin landscape in white adipose tissue suggest humans may have less beigeing potential than other primates
Devjanee Swain Swain Lenz, Alejandro Berrio, Alexias Saffi, Gregory E Crawford, Gregory Wray
Humans carry a much larger percentage of body fat than other primates. Despite the central role of adipose tissue in metabolism, little is known about the evolution of white adipose tissue in primates. Phenotypic divergence is often caused by genetic divergence in cis-regulatory regions. We examined the cis-regulatory landscape of fat during human origins by performing comparative analyses of chromatin accessibility in human and chimpanzee adipose tissue using macaque as an outgroup. We find that many cis-regulatory regions that are specifically closed in humans are under positive selection, located near genes involved with lipid metabolism, and contain a short sequence motif involved in the beigeing of fat, the process in which white adipocytes are transdifferentiated into beige adipocytes. While the primary role of white adipocytes is to store lipids, beige adipocytes are thermogeneic. The collective closing of many putative regulatory regions associated with beiging of fat suggests an adaptive mechanism that increases body fat...
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DanielJDrucker: Should you keep an open mind about the therapetic potential of human beige adipose tissue #obesity when the chromatin is closed? https://t.co/5BkqV4ggKu
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Authors: 5
Total Words: 6495
Unqiue Words: 1902

2.003 Mikeys
#4. The evolution of collective infectious units in viruses
Asher Leeks, Rafael Sanjuán, Stuart A. West
Viruses frequently spread among cells or hosts in groups, with multiple viral genomes inside the same infectious unit. These collective infectious units can consist of multiple viral genomes inside the same virion, or multiple virions inside a larger structure such as a vesicle. Collective infectious units deliver multiple viral genomes to the same cell simultaneously, which can have important implications for viral pathogenesis, antiviral resistance, and social evolution. However, little is known about why some viruses transmit in collective infectious units, whereas others do not. We used a simple evolutionary approach to model the potential costs and benefits of transmitting in a collective infectious unit. We found that collective infectious units could be favoured if cells infected by multiple viral genomes were significantly more productive than cells infected by just one viral genome, and especially if there were also efficiency benefits to packaging multiple viral genomes inside the same infectious unit. We also found that...
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AsherLeeks: New preprint out! We modelled some reasons why viruses sometimes disperse in groups (as part of collective infectious units). https://t.co/vfSV3eYGNR
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Authors: 3
Total Words: 8595
Unqiue Words: 2009

2.002 Mikeys
#5. Widespread selection for high and low secondary structure in coding sequences across all domains of life
Daniel Gebert, Julia Jehn, David Rosenkranz
Codon composition, GC-content and local RNA secondary structures can have a profound effect on gene expression and mutations affecting these parameters, even though they do not alter the protein sequence, are not neutral in terms of selection. Although evidence exists that in some cases selection favors more stable RNA secondary structures, we currently lack a concrete idea of how many genes are affected within a species, and if this is a universal phenomenon in nature. We searched for signs of structural selection in a global manner, analyzing a set of one million coding sequences from 73 species representing all domains of life, as well as viruses, by means of our newly developed software PACKEIS. We show that codon composition and amino acid identity are main determinants of RNA secondary structure. In addition, we show that the arrangement of synonymous codons within coding sequences is non-random, yielding extremely high, but also extremely low secondary structures significantly more often than expected by chance. Together,...
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smallRNA_Mainz: Check out our latest preprint: Widespread selection for high and low secondary structure in coding sequences across all domains of life. https://t.co/vBPUNnxxLq
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Sample Sizes : [100, 244314, 33, 20, 20]
Authors: 3
Total Words: 6526
Unqiue Words: 1905

2.001 Mikeys
#6. A next generation approach to species delimitation reveals the role of hybridization in a cryptic species complex of corals
Andrea M. Quattrini, Tiana Wu, Keryea Soong, Ming-Shiou Jeng, Yehuda Benayahu, Catherine S. McFadden
Background: Our ability to investigate processes shaping the evolutionary diversification of corals (Cnidaria: Anthozoa) is limited by a lack of understanding of species boundaries. Discerning species has been challenging due to a multitude of factors, including homoplasious and plastic morphological characters and the use of molecular markers that are either not informative or have not completely sorted. Hybridization can also blur species boundaries by leading to incongruence between morphology and genetics. We used traditional DNA barcoding and restriction-site associated DNA sequencing combined with coalescence-based and allele-frequency methods to elucidate species boundaries and simultaneously examine the potential role of hybridization in a speciose genus of octocoral, Sinularia. Results: Species delimitations using two widely used DNA barcode markers, mtMutS and 28S rDNA, were incongruent with one another and with the morphospecies identifications, likely due to incomplete lineage sorting. In contrast, 12 of the 15...
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razibkhan: A next generation approach to species delimitation reveals the role of hybridization in a cryptic species complex of corals https://t.co/BfAxyi2lFr #evolution
reef_combo: Hybridization and species delimitation in octocorals https://t.co/UvMlhZdh5F
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Sample Sizes : [1000]
Authors: 6
Total Words: 16260
Unqiue Words: 4985

1.998 Mikeys
#7. Consistency of SVDQuartets and Maximum Likelihood for Coalescent-based Species Tree Estimation
Matthew Wascher, Laura Kubatko
Numerous methods for inferring species-level phylogenies under the coalescent model have been proposed within the last 20 years, and debates continue about the relative strengths and weaknesses of these methods. The approaches taken by these methods can be classified into three groups. Summary methods carry out inference for multilocus data by first computing a summary statistic for each locus, and then forming an estimate of the species phylogeny using these single-locus summaries as input. Such methods are often criticized for failing to account for uncertainty in the estimates computed for each locus in the second stage of the analysis. The second class of methods have been referred to as "full data methods" because they utilize the sequence data directly by carrying out estimation in a Bayesian framework, with specific implementations designed to handle either multilocus or SNP data. Because such methods require both computation of the likelihood and Markov chain Monte Carlo for inference, they are limited in the size of the...
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biorxivpreprint: Consistency of SVDQuartets and Maximum Likelihood for Coalescent-based Species Tree Estimation https://t.co/GZv1QSKtMu #bioRxiv
biorxiv_evobio: Consistency of SVDQuartets and Maximum Likelihood for Coalescent-based Species Tree Estimation https://t.co/knA8baOwuk #biorxiv_evobio
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Sample Sizes : None.
Authors: 2
Total Words: 8616
Unqiue Words: 1873

1.998 Mikeys
#8. Divergence of piRNA pathway proteins affects piRNA biogenesis but not TE transcript level
Luyang Wang, Daniel Barbash, Erin Kelleher
SUMMARY In metazoan germlines, the piRNA pathway acts as a genomic immune system: employing small-RNA mediated silencing to defend host DNA from the harmful effects of transposable elements (TEs). In response to dynamic changes in genomic TE content, host genomes are proposed to alter the piRNAs that they produce in order to silence the most active TE families. However, piRNA pathway proteins, which execute piRNA biogenesis and enforce silencing of targeted sequences, also evolve rapidly and adaptively in animals. If TE silencing evolves through changes in piRNAs, what necessitates changes in piRNA pathway proteins? Here we used interspecific complementation to test for functional differences between Drosophila melanogaster and D. simulans alleles of three adaptively evolving piRNA pathway proteins: Armitage, Aubergine and Spindle-E. Surprisingly, we find very few differences in TE transcript levels, but global effects on piRNA biogenesis, particularly for Armitage. Therefore, despite the fitness costs of transposition, piRNA...
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biorxivpreprint: Divergence of piRNA pathway proteins affects piRNA biogenesis but not TE transcript level https://t.co/J4pksAhqNG #bioRxiv
biorxiv_evobio: Divergence of piRNA pathway proteins affects piRNA biogenesis but not TE transcript level https://t.co/Lv60Nikhtx #biorxiv_evobio
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Authors: 3
Total Words: 9092
Unqiue Words: 2419

1.998 Mikeys
#9. Population persistence under high mutation rate: from evolutionary rescue to lethal mutagenesis
Yoann Anciaux, Amaury Lambert, Oph&eacutelie Ronce, Lionel Roques, Guillaume Martin
Populations may genetically adapt to severe stress that would otherwise cause their extirpation. Recent theoretical work, combining stochastic demography with Fisher′s Geometric Model of adaptation, has shown how evolutionary rescue becomes unlikely beyond some critical intensity of stress. Increasing mutation rates may however allow adaptation to more intense stress, raising concerns about the effectiveness of treatments against pathogens. This previous work assumes that populations are rescued by the rise of a single resistance mutation. However, even in asexual organisms, rescue can also stem from the accumulation of multiple mutations in a single genome. Here, we extend this model to study the rescue process in an asexual population where the mutation rate is sufficiently high so that such events may be common. We predict both the ultimate extinction probability of the population and the distribution of extinction times. We compare the accuracy of different approximations covering a large range of mutation rates. Moderate...
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biorxivpreprint: Population persistence under high mutation rate: from evolutionary rescue to lethal mutagenesis https://t.co/ACvuCfSCad #bioRxiv
biorxiv_evobio: Population persistence under high mutation rate: from evolutionary rescue to lethal mutagenesis https://t.co/hENsAhZLuB #biorxiv_evobio
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Authors: 5
Total Words: 12521
Unqiue Words: 3385

1.998 Mikeys
#10. Eco-evolutionary feedbacks between predator's linkage disequilibrium and prey densities maintain diversity
Swati Patel, Reinhard Buerger
Diversity occurs at multiple scales. Within a single population, there is diversity in genotypes and phenotypes. At a larger scale, within ecological communities, there is diversity in species. There have been a number of studies to investigate how diversity at these two scales influence each other through what has been termed eco-evolutionary feedbacks. Here we study a three-species ecological module called apparent competition, in which the predator is evolving in a trait that determines its interaction with two prey species. Unlike previous studies on apparent competition, which employed evolutionary frameworks with greatly simplified genetics, we study a multilocus eco-evolutionary model in which the predator's evolving trait is determined by two diallelic loci. We ask how eco-evolutionary feedbacks with these two loci affect the coexistence of the prey species and the maintenance of polymorphisms within the predator species. In doing so, we uncover a novel eco-evolutionary feedback between the prey species and the linkage...
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biorxivpreprint: Eco-evolutionary feedbacks between predator's linkage disequilibrium and prey densities maintain diversity https://t.co/xCKEdw2j3s #bioRxiv
biorxiv_evobio: Eco-evolutionary feedbacks between predator's linkage disequilibrium and prey densities maintain diversity https://t.co/dhxWnEyV4y #biorxiv_evobio
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Sample Sizes : None.
Authors: 2
Total Words: 15352
Unqiue Words: 2707

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