bioRxiv - Evolutionary Biology最新文献

{"title":"Grains, trade and war in the multimodal transmission of Rice yellow mottle virus: an historical and phylogeographical retrospective","authors":"Innocent Ndikumana, Geoffrey Onaga, Agnes Pinel-Galzi, Pauline Rocu, Judith Hubert, Hassan Karakacha Were, Antony Adego, Mariam Nyongesa Were, Nils Poulicard, Maxime Hebrard, Simon Dellicour, Philippe Lemey, Erik Gilbert, Marie-Jose Dugue, Francois Chevenet, Paul Bastide, Stephane Guindon, Denis Fargette, Eugenie Hebrard","doi":"10.1101/2024.08.20.608750","DOIUrl":"https://doi.org/10.1101/2024.08.20.608750","url":null,"abstract":"Rice yellow mottle virus (RYMV) is a major pathogen of rice in Africa. RYMV has a narrow host range limited to rice and a few related poaceae species. We explore the links between the spread of RYMV in East Africa and rice history since the second half of the 19th century. The phylogeography of RYMV in East Africa was reconstructed from coat protein gene sequences (ORF4) of 335 isolates sampled over two million square kilometers between 1966 and 2020. Dispersal patterns obtained from ORF2a and ORF2b, and full-length sequences converged to the same scenario. The following imprints of rice cultivation on RYMV epidemiology were unveiled. RYMV emerged in the middle of the 19th century in the Eastern Arc Mountains where slash-and-burn rice cultivation was practiced. Several spillovers from wild hosts to cultivated rice occurred. RYMV was then rapidly introduced into the adjacent large rice growing Kilombero valley. Harvested seeds are contaminated by debris of virus infected plants that subsist after threshing and winnowing. Long-distance dispersal of RYMV is consistent (i) with rice introduction along the caravan routes from the Indian Ocean Coast to Lake Victoria in the second half of the 19th century, (ii) seed movement from East Africa to West Africa at the end of the 19th century, from Lake Victoria to the north of Ethiopia in the second half of the 20th century and to Madagascar at the end of the 20th century, (iii) and, unexpectedly, with rice transport at the end of the First World War as a troop staple food from the Kilombero valley towards the South of Lake Malawi. Overall, RYMV dispersal was associated to a broad range of human activities, some unsuspected. Consequently, RYMV has a wide dispersal capacity, its dispersal metrics estimated from phylogeographic reconstructions are similar to those of highly mobile zoonotic viruses.","PeriodicalId":501183,"journal":{"name":"bioRxiv - Evolutionary Biology","volume":"117 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142205413","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Climatic-environmental influences on hominin brain size over the last 5 million years","authors":"Samuel L Nicholson, Thomas Puschel, Joanna Baker, Chris Venditti","doi":"10.1101/2024.09.09.611970","DOIUrl":"https://doi.org/10.1101/2024.09.09.611970","url":null,"abstract":"A large brain relative to body mass is considered a distinguishing hominin trait. It has frequently been related to a suite of social, behavioral, technological, and other cognitive adaptations that differentiate humans from other species. The processes underlying large brain size evolution have therefore been a subject of rigorous scientific debate. Many hypotheses have been proposed to explain how climate and environment drive the selection of larger brain sizes, but monotonic influences of climate-environmental selective pressures are often assumed and rarely have between- and within-species effects been considered. Here, we apply Bayesian phylogenetic comparative techniques to the hominin fossil record to test the effect of climatic and environmental pressures (C-E) on brain size evolution, whilst simultaneously accounting for body mass and chronological age. We find that colder and more variable temperatures have a positive within-species effect on brain size evolution, likely related to biological adaptations to mitigate against hypothermia. However, in Homo, the strength of this effect diminishes over time suggesting that in later species (Homo sapiens and Homo neanderthalensis) brain sizes were less affected by C-E conditions.","PeriodicalId":501183,"journal":{"name":"bioRxiv - Evolutionary Biology","volume":"309 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142205445","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evolution of venom production in marine predatory snails","authors":"Giulia Zancolli, Maria Vittoria Modica, Nicolas Puilladre, Yuri Kantor, Agneesh Barua, Giulia Campli, Marc Robinson-Rechavi","doi":"10.1101/2024.09.09.612013","DOIUrl":"https://doi.org/10.1101/2024.09.09.612013","url":null,"abstract":"Venom is a widespread secretion in nature, extensively studied for its toxin components and application potential. Yet, the evolution of venom production remains poorly understood. To address this question, we conducted a comparative transcriptomics analysis of the oesophagus-associated glands in marine predatory gastropods, among which the cone snail venom gland represents a pinnacle of specialisation. We found that the functional divergence and specialisation of the venom gland was achieved through a redistribution of its ancestral digestive functions to other organs, specifically the oesophagus. This entailed concerted expression changes and accelerated transcriptome evolution across the entire digestive system. The increase in venom gland secretory capacity was achieved through the modulation of an ancient secretory machinery, particularly genes involved in endoplasmic reticulum stress and unfolded protein response. On the other hand, the emergence of novel genes, involving transposable elements, contributed to the gland regulatory network. Our analysis provides new insights into the genetic basis of functional divergence and highlights the remarkable plasticity of the gastropod digestive system.","PeriodicalId":501183,"journal":{"name":"bioRxiv - Evolutionary Biology","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142205417","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Importance of Nonsense Errors: Estimating the Rate and Implications of Drop-Off Errors during Protein Synthesis","authors":"Alexander L Cope, Denizhan Pak, Michael A Gilchrist","doi":"10.1101/2024.09.05.611510","DOIUrl":"https://doi.org/10.1101/2024.09.05.611510","url":null,"abstract":"The process of mRNA translation is both energetically costly and relatively error-prone compared to transcription and replication. Nonsense errors during mRNA translation occur when a ribosome drops off a transcript before reaching a stop codon, resulting in energetic investment in an incomplete and likely non-functional protein. Nonsense errors impose a potentially significant energy burden on the cell, making it critical to quantify their frequency and energetic cost. Here, we present a model of ribosome movement for estimating protein production, elongation, and nonsense error rates from high-throughput ribosome profiling data. Applying this model to an exemplary ribosome profiling dataset in S. cerevisiae, we find that nonsense error rates vary between codons, in conflict with the general assumption of uniform rates across sense codons. Using our parameter estimates, we find multiple lines of evidence that selection against nonsense errors is a prominent force shaping coding-sequence evolution, including that nonsense errors place an energetic burden on cells comparable to ribosome pausing. Our results indicate greater consideration should be given to the impact of nonsense errors in shaping coding-sequence evolution.","PeriodicalId":501183,"journal":{"name":"bioRxiv - Evolutionary Biology","volume":"19 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142205415","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"FishPi: a bioinformatic prediction tool to link piRNA and transposable elements in zebrafish","authors":"Alice May Godden, Benjamin Rix, Simone Immler","doi":"10.1101/2024.09.10.612046","DOIUrl":"https://doi.org/10.1101/2024.09.10.612046","url":null,"abstract":"Background: Piwi-interacting RNAs (piRNA)s are non-coding small RNAs that post-transcriptionally affect gene expression and regulation. Through complementary seed region binding with transposable elements (TEs), piRNAs protect the genome from transposition, and therefore a tool to link piRNAs with complementary TE targets is needed. Tools like TEsmall can process sRNA-seq datasets to produce differentially expressed piRNAs and piRScan developed for nematodes can link piRNAs and TEs but it requires the user to know the target region of interest and work backwards. Results: We have therefore developed FishPi to predict the pairings between piRNA and TEs. FishPi works with individual piRNAs or a list of piRNA sequences in fasta format. The software focuses on the piRNA:TE seed region and analyses reference TEs for piRNA complementarity. TE type is examined, counted and stored to a dictionary, with genomic loci recorded. Any updates to piRNA-TE binding rules, can easily be incorporated by updating the code underlying FishPi. FishPi provides a graphic interface, using tkinter, that requires the user to input piRNA sequences to generate comprehensive reports on piRNA:TE dynamics. FishPi can easily be adapted to other genomes opening the interpretation of piRNA functionality to a wide community. Conclusions: Users will gain insight into genome age and FishPi will help further our understanding of the biological role of piRNAs and their interaction with TEs in a similar way that public databases have improved the access to and the understanding of the role of small RNAs.","PeriodicalId":501183,"journal":{"name":"bioRxiv - Evolutionary Biology","volume":"59 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142205416","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The High Arctic is dominated by uncharacterized, genetically highly diverse bacteriophages","authors":"Audree Lemieux, Alexandre J Poulain, Stephane Aris-Brosou","doi":"10.1101/2024.09.10.612304","DOIUrl":"https://doi.org/10.1101/2024.09.10.612304","url":null,"abstract":"While the Earth's virosphere is estimated to be in the range of 10^31 viral particles, the vast majority of its diversity has yet to be discovered. In recent years, metagenomics has rapidly allowed the identification of viruses, from microenvironments to extreme environments like the High Arctic. However, the High Arctic virome is largely composed of viral sequences that have few, if any, matches to classified viruses in existing databases. Here, to bypass limitations posed by similarity-based strategies, we resorted to a metagenomics approach that placed viral genes found in Lake Hazen, a High Arctic lake, in a phylogenetic context with known viruses. We show that while High Arctic viruses clustered with known bacteriophages, they have undergone unique evolutionary processes characterized by high evolutionary rates, making them distinct from and more diverse than known viruses. A better understanding of how viruses from extreme polar conditions adapt and evolve could help us gain insights on the viral response to climate change and other environmental stressors.","PeriodicalId":501183,"journal":{"name":"bioRxiv - Evolutionary Biology","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142205418","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Functional insights into the effect of feralisation on the gut microbiota of cats worldwide","authors":"Ostaizka Aizpurua, Amanda Bolt Botnen, Raphael Eisenhofer, Inaki Odriozola, Luisa Santos-Bay, Mads Bjorn Bjornsen, M Thomas P Gilbert, Antton Alberdi","doi":"10.1101/2024.09.04.611329","DOIUrl":"https://doi.org/10.1101/2024.09.04.611329","url":null,"abstract":"Feralisation, the process by which domesticated organisms revert to a wild state, is a widespread phenomenon across various species. Successfully adapting to a new environment with different access to food, shelter, and other resources requires rapid physiological and behavioural changes, which could potentially be facilitated by gut microbiota plasticity. To investigate whether alterations in gut microbiota support this transition to a feral lifestyle, we analysed the gut microbiomes of domestic and feral cats from six geographically diverse locations using genome-resolved metagenomics. By reconstructing 229 draft genomes from 92 cats, we identified a typical carnivore microbiome structure, with notable diversity and taxonomic differences across regions. While overall diversity metrics did not differ significantly between domestic and feral cats, hierarchical modelling of species communities, accounting for geographic and sex covariates, revealed distinct taxonomic and functional profiles between the two groups. While taxonomic enrichment was balanced, microbial functional capacities were significantly enriched in feral cats. These functional enhancements, particularly in amino acid and lipid degradation, correspond to feral cats' dietary reliance on crude protein and fat. Additionally, functional differences were consistent with behavioural contrasts, such as the more aggressive and elusive behaviour measured in feral cats compared to the docile behaviour of domestic cats. Finally, the observed enrichment in short-chain fatty acid, neurotransmitter, and vitamin B12 production in feral cats aligns with improved cognitive function and potentially contributes to their heightened aggression and elusiveness. Our findings suggest that microbiome shifts may play a significant role in the development of physiological and behavioural traits advantageous for a feral lifestyle, supporting the adaptive success of feral cats in the wild.","PeriodicalId":501183,"journal":{"name":"bioRxiv - Evolutionary Biology","volume":"12 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142205421","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evolution is coupled with branching across many granularities of life","authors":"Jordan Douglas, Remco Bouckaert, Simon C Harris, Charles W Carter, Peter R Wills","doi":"10.1101/2024.09.08.611933","DOIUrl":"https://doi.org/10.1101/2024.09.08.611933","url":null,"abstract":"Across many different scales of life, the rate of evolutionary change is often accelerated at the time when one lineage splits into two. The emergence of novel protein function can be facilitated by gene duplication (neofunctionalisation); rapid morphological change is often accompanied with speciation (punctuated equilibrium); and the establishment of cultural identity is frequently driven by sociopolitical division (schismogenesis). In each case, the change resists re-homogenisation; promoting assortment into distinct lineages that are susceptible to different selective pressures, leading to rapid divergence. The traditional gradualistic view of evolution struggles to detect this phenomenon. We have devised a probabilistic framework that constructs phylogenies, tests hypotheses, and improves divergence time estimation when evolutionary bursts are present. As well as assigning a clock rate of gradual evolution to each branch of a tree, this model also assigns a spike of abrupt change, and independently estimates the contributions arising from each process. We provide evidence of abrupt evolution at the time of branching for proteins (aminoacyl-tRNA synthetases), animal morphologies (cephalopods), and human languages (Indo-European). These three cases provide unique insights: for aminoacyl-tRNA synthetases, the trees are substantially different from those obtained under gradualist models; Cephalopod morphologies are found to evolve almost exclusively through abrupt shifts; and Indo-European dispersal is estimated to have started around 6000 BCE, corroborating the recently proposed hybrid explanation. This work demonstrates a robust means for detecting burst-like processes, and advances our understanding of the link between evolutionary change and branching events. Our open-source code is available under a GPL license.","PeriodicalId":501183,"journal":{"name":"bioRxiv - Evolutionary Biology","volume":"23 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142205420","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Selection efficacy differs between lifestages in the haploid-diploid Marchantia polymorpha subsp. ruderalis","authors":"Tianyu Shen, Philippe Gadient, Justin Goodrich, Hannes Becher","doi":"10.1101/2024.09.06.611587","DOIUrl":"https://doi.org/10.1101/2024.09.06.611587","url":null,"abstract":"Ploidy has profound effects on evolution. Perhaps the most compelling effect is related to dominance: In cells with more than one genome copy, the effects of non-dominant deleterious variants are 'masked' to some extent, leading to a reduction in the efficacy of selection. This, in turn, leads to increased levels of nucleotide diversity, and it may also affect nucleotide substitution rates.\u0000To test this predicted association between ploidy and the efficacy of selection, we studied genome scale per-gene patterns of genetic diversity and divergence in the genome of the haploid-diploid bryophyte Marchantia. We treated lifestage gene expression bias as a continuous covariate and accounted for genomic autocorrelation patterns using smoothing splines in a general additive regression model (GAM) framework.\u0000Consistent with a lower efficacy of purifying selection, we found increased levels of sequence diversity, Watterson's theta, and net divergence at non-degenerate sites in genes with diploid-biased gene expression. These genes also showed reduced levels of codon usage bias. In addition, we found chromosome 5 to be an outlier with overall decreased levels of diversity, the site-frequency spectrum skewed towards common alleles, and increased linkage disequilibrium.\u0000In this study, we show the utility of generalized additive models in population genomics, and we present evidence for a ploidy associated difference in the efficacy of selection. We discuss parallels to the evolution of (diploid) sex chromosomes and why the patterns observed are unlikely to be mediated by masking.","PeriodicalId":501183,"journal":{"name":"bioRxiv - Evolutionary Biology","volume":"22 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142205443","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evolutionary and Functional Analysis of Monoamine Oxidase C (MAO C): A Novel Member of the MAO Gene Family","authors":"Gianluca Merello, Montserrat Olivares-Costa, Lorenzo Basile, Tammy P. Pastor, Pablo Mendoza-Soto, Luis Padilla-Santiago, Gonzalo Mardones, Claudia Binda, Juan C. Opazo","doi":"10.1101/2024.08.20.608864","DOIUrl":"https://doi.org/10.1101/2024.08.20.608864","url":null,"abstract":"The monoamine oxidase (MAO) gene family encodes for enzymes that perform the oxidative deamination of monoamines, a process required to degrade norepinephrine, serotonin, dopamine, and other amines. While mammalian MAO enzymes, MAO A and MAO B, have been extensively studied, the molecular properties of the other family members are only partly uncovered. This study aims to explore the evolution of monoamine oxidases, emphasizing understanding the MAO gene repertoire among vertebrates. Our analyses show that the duplication that gave rise to MAO A and MAO B occurred in the ancestor of tetrapods, between 408 and 352 million years ago. Non-tetrapod jawed vertebrates possess the ancestral preduplicative condition of MAO A/B. Our results also identified a new family member, MAO C, in non-tetrapod jawed vertebrates. Thus, most jawed vertebrates possess a repertoire of two MAO genes, MAO A and MAO B in tetrapods and MAO A/B and MAO C in non-tetrapod jawed vertebrates, representing different MAO gene lineages. Jawless vertebrates possess the ancestral condition of a single copy gene, MAO A/B/C. Enzymatic assays conducted on the MAO recombinant enzymes of the Indo-Pacific tarpon show that both proteins, MAO A/B and MAO C, have enzymatic and molecular properties more similar to human MAO A, with the former featuring a strikingly higher activity rate when compared to all other MAO enzymes. Our analyses underscore the importance of scanning the tree of life for new gene lineages to understand phenotypic diversity and gain detailed insights into their function.","PeriodicalId":501183,"journal":{"name":"bioRxiv - Evolutionary Biology","volume":"11 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142205419","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}