Top 10 Biorxiv Papers Today in Evolutionary Biology


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#1. Genome-wide search for parent-of-origin allele specific expression in Bombus terrestris.
Hollie Marshall, Jelle S van Zweden, Anneleen Van Geystelen, Kristof Benaets, Felix Wäckers, Eamonn B Mallon, Tom Wenseleers
Genomic imprinting is the expression bias of one allele in a diploid organism, expression being dependent upon which parent the allele was inherited from. Haig's kinship theory predicts that genomic imprinting occurs due to an evolutionary conflict-of-interest between the maternal alleles and paternal alleles of an individual. In social insects, it has been suggested that genomic imprinting should be widespread. One recent study identified parent-of-origin gene expression in honeybees and found evidence supporting one prediction of Haig's kinship theory. However, very little is known about genomic imprinting in insects and multiple theoretical predictions must be tested to avoid single-study confirmation bias. We therefore decided to test if parent-of-origin gene expression also occurs in another social bee using reciprocal crosses. We found equal numbers of maternally and paternally expressed alleles in both reproductive and sterile workers with the majority of genes showing the same expression bias in both castes. The most...
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Authors: 7
Total Words: 9598
Unqiue Words: 2968

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#2. Efficient inference, potential, and limitations of site-specific substitution model
Vadim Puller, Pavel Sagulenko, Richard Neher
Natural selection imposes a complex filter on which variants persist in a population resulting in evolutionary patterns that vary greatly along the genome. Some sites evolve close to neutrally, while others are highly conserved, allow only specific states or only change in concert with other sites. Most commonly used evolutionary models, however, ignore much of this complexity and at best account for variation in the rate at which different sites change. Here, we present an efficient algorithm to estimate more complex models that allow for site-specific preferences and explore the accuracy at which such models can be estimated from simulated data. We find that an iterative approximate maximum likelihood scheme uses information in the data efficiently and accurately estimates site-specific preferences from large data sets with moderately diverged sequences. Ignoring site-specific preferences during estimation of branch length of phylogenetic trees -- an assumption of most phylogeny software -- results in substantial underestimation...
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PetrovADmitri: RT @biorxivpreprint: Efficient inference, potential, and limitations of site-specific substitution model https://t.co/TsYQ5tuimV #bioRxiv
salazarbiol: RT @biorxiv_evobio: Efficient inference, potential, and limitations of site-specific substitution model https://t.co/38DlP9ZV2C #biorxiv_e…
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#3. The Deep(er) Roots of Eukaryotes and Akaryotes
Ajith Harish, David A. Morrison
Locating the root-node of the "tree of life" (ToL) is one of the hardest problems in phylogenetics. The root-node or the universal common ancestor (UCA) divides the descendants into organismal domains. Two notable variants of the two-domains ToL (2D-ToL) have gained support recently, though, Williams and colleagues (W&C) claim that one is better supported than the other. Here, we argue that important aspects of estimating evolutionary relatedness and assessing phylogenetic signal in empirical data were overlooked. We focus on phylogenetic character reconstructions necessary to describe the UCA or its closest descendants in the absence of reliable fossils. It is well known that different character-types present different perspectives on evolutionary history that relate to different phylogenetic depths. Which of the 2D-ToL hypotheses is better supported depends on which kind of molecular features -- protein-domains or their component amino-acids -- are better for resolving the common ancestors (CA) at the roots of clades. In...
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biorxivpreprint: The Deep(er) Roots of Eukaryotes and Akaryotes https://t.co/fzubtoCHkg #bioRxiv
biorxiv_evobio: The Deep(er) Roots of Eukaryotes and Akaryotes https://t.co/zvZhC2AtPh #biorxiv_evobio
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Authors: 2
Total Words: 3013
Unqiue Words: 1336

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#4. On the origin and evolution of RNA editing in metazoans
Qiye Li, Pei Zhang, Ji Li, Hao Yu, Xiaoyu Zhan, Yuanzhen Zhu, Qunfei Guo, Huishuang Tan, Nina Lundholm, Lydia Garcia, Michael D. Martin, Meritxell Antó Subirats, Yi-Hsien Su, Iñaki Ruiz-Trillo, Mark Q. Martindale, Jr-Kai Yu, M. Thomas P. Gilbert, Guojie Zhang
Extensive adenosine-to-inosine (A-to-I) editing of nuclear-transcribed RNAs is the hallmark of metazoan transcriptional regulation, and is fundamental to numerous biochemical processes. Here we explore the origin and evolution of this regulatory innovation, by quantifying its prevalence in 22 species that represent all major transitions in metazoan evolution. We provide substantial evidence that extensive RNA editing emerged in the common ancestor of extant metazoans. We find the frequency of RNA editing varies across taxa in a manner independent of metazoan complexity. Nevertheless, cis-acting features that guide A-to-I editing are under strong constraint across all metazoans. RNA editing seems to preserve an ancient mechanism for suppressing the more recently evolved repetitive elements, and is generally nonadaptive in protein-coding regions across metazoans, except for Drosophila and cephalopods. Interestingly, RNA editing preferentially target genes involved in neurotransmission, cellular communication and cytoskeleton, and...
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stemdevevo: RT @biorxivpreprint: On the origin and evolution of RNA editing in metazoans https://t.co/9H2rrcMTRg #bioRxiv
TonyBurnetti: RT @biorxiv_evobio: On the origin and evolution of RNA editing in metazoans https://t.co/39iXY9W1a9 #biorxiv_evobio
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#5. Quantitative genetics of temperature performance curves of Neurospora crassa
Neda N Moghadam, Karendeep Sidhu, Pauliina A M Summanen, Tarmo Ketola, Ilkka Kronholm
Earth's temperature is increasing due to anthropogenic CO2 emissions; and organisms need either to adapt to higher temperatures, migrate into colder areas, or face extinction. Temperature affects nearly all aspects of organism's physiology via its influence on metabolic rate and protein structure. Compared to other abiotic stresses, genetic adaptation to increased temperature may be much harder to achieve due to systemic effects of temperature. As the evolutionary potential for adaptation to higher temperatures is relatively unknown, we studied the quantitative genetics of thermal performance curves of the fungal model system Neurospora crassa . We asked whether there is genetic variation for thermal performance curves and examined possible genetic of evolution constraints by estimating the G -matrix. We observed substantial amount of genetic variation for growth in different temperatures, and most genetic variation was for performance curve elevation. Contrary to common theoretical assumptions we did not find strong evidence for...
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biorxivpreprint: Quantitative genetics of temperature performance curves of Neurospora crassa https://t.co/6YmCeMhLGV #bioRxiv
biorxiv_evobio: Quantitative genetics of temperature performance curves of Neurospora crassa https://t.co/3E3XAITddW #biorxiv_evobio
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#6. The relationship between longevity and diet is genotype dependent and sensitive to desiccation
Andrew W McCracken, Eleanor Buckle, Mirre JP Simons
Dietary restriction (DR) is a key focus in ageing research. Specific conditions and genotypes were recently found to negate lifespan extension by DR, questioning the universal relevance of DR. However, the conceptual framework of dietary reaction norms explains why DRs effects might not be apparent in some situations. When dietary reaction norms shift with genetic or environmental effects, a specific dyad of diets tested can result in a null effect. Only if a full reaction norm is tested can lifespan (or any trait) be shown to be refractory to diet. We tested comprehensively, for the first time, the importance of dietary reaction norms by measuring longevity and fecundity on five diets in five genotypes, with and without water supplementation, using high sample sizes in the fly (N>25,000). We detected substantial genetic variation in the reaction norm between diet and lifespan. Environments supplemented with water rescued putative desiccation stress but only at the richest diets. Fecundity declined at these richest diets, but...
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Total Words: 6533
Unqiue Words: 1916

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#7. Contrasting population structure and demographic history of cereal aphids in different environmental and agricultural landscapes
Ramiro Morales-Hojas, Jingxuan Sun, Fernando Alvira Iraizoz, Xiaoling Tan, Julian Chen
Genetic diversity of populations has important ecological and evolutionary consequences, which are fundamental to improve the sustainability of agricultural production. Studies of how differences in agricultural management and environment influence the population structure of insect pests are fundamental to predict outbreaks and optimise control programmes. Here, we have studied the population genetic diversity and evolution of Sitobion avenae and Sitobion miscanthi (previously mistaken for S. avenae ), which are among the most relevant aphid pests of cereals across Europe and China, respectively. We have used a genomic approach that allows the identification of weak geographic structure and migration patterns at scales that were previously not discernible. In the present study, we show that the population structure in present day populations are different from that described in previous studies, which suggests that they have evolved recently possibly as a response to human-induced changes in agriculture. In the UK, S. avenae is...
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#8. Wing shape and environmental energy are associated with molecular evolutionary rates in a large avian radiation
David A. Duchene, Paola A Valencia, Daniel A. Cadena
Among the macroevolutionary drivers of molecular evolutionary rates, metabolic demands and environmental energy have been a central topic of discussion. The large number of studies examining these associations have found mixed results, and have rarely explored the interactions among various factors impacting molecular evolutionary rates. Taking the diverse avian family Furnariidae as a case study, we examined the association between several estimates of molecular evolutionary rates with a proxy of metabolic demands imposed by flight (wing morphology) and proxies of environmental energy across the geographic ranges of species (temperature and UV radiation). We found a strong positive association between molecular rates in genomic regions that can change the coded amino-acid with wing morphology, environmental temperature, and UV radiation. Strikingly, however, we did not find evidence of such associations with molecular rates at sites not impacting amino-acids. Our results suggest that the demands of flight and environmental energy...
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Repository: furnariidae_rates
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Total Words: 9005
Unqiue Words: 3144

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#9. Convergent genetic architecture underlies parallel pelvic reduction in genetically highly structured stickleback species
Petri M Kemppainen, Zitong Li, Pasi Rastas, Ari Loytynoja, Bohao Fang, Baocheng Guo, Takahito Shikano, Jing Yang, Juha Merila
Repeated and independent evolution of the same phenotypes in similar environments is common, but less is known about the repeatability of the underlying genetic mechanisms, particularly in species with small effective population sizes and strong population structuring. We identified genomic regions responsible for the repeated reduction of pelvic spines and girdles in three crosses between pond (reduced pelvic apparatus) and marine (full apparatus) nine-spined sticklebacks (Pungitius pungitius) using quantitative trait locus (QTL) mapping. In one cross both traits mapped to linkage group 7 (LG7), where the gene Pituitary homeobox transcription factor 1 (Pitx1) is known to be associated with pelvic reduction. In the other two crosses, pelvic reduction was polygenic and the nine out of the ten novel QTL (explaining 3-10% of the total phenotypic variation) were all unique to one of the three crosses. We further screened whole genomes from 27 different populations for the presence of deletions in Pitx1 regulatory element (Pel) which,...
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#10. Radula diversification promotes ecomorph divergence in an adaptive radiation of freshwater snails
Leon Hilgers, Stefanie Hartmann, Jobst Pfaender, Nora Lentge-Maaß, Thomas von Rintelen, Michael Hofreiter
Adaptive diversification of complex traits plays a pivotal role for the evolution of organismal diversity. However, the underlying molecular mechanisms remain largely elusive. In the freshwater snail genus Tylomelania, adaptive radiations were likely promoted by trophic specialization via diversification of their key foraging organ, the radula. To investigate the molecular basis of radula diversification and its contribution to lineage divergence, we use pooled tissue-specific transcriptomes of two sympatric Tylomelania sarasinorum ecomorphs. We show that divergence in both gene expression and coding sequences is stronger between radula transcriptomes compared to mantle and foot transcriptomes. These findings support the hypothesis that diversifying selection on the radula is driving speciation in Tylomelania radiations. We also identify several candidate genes for radula divergence. Putative homologs of some candidates (hh, arx, gbb) also contributed to trophic specialization in cichlids and Darwin's finches, indicating that some...
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