Pub Date : 2024-09-11DOI: 10.1101/2024.08.20.608750
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
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.
{"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}
Pub Date : 2024-09-10DOI: 10.1101/2024.09.09.611970
Samuel L Nicholson, Thomas Puschel, Joanna Baker, Chris Venditti
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.
{"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}
Pub Date : 2024-09-10DOI: 10.1101/2024.09.09.612013
Giulia Zancolli, Maria Vittoria Modica, Nicolas Puilladre, Yuri Kantor, Agneesh Barua, Giulia Campli, Marc Robinson-Rechavi
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.
{"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}
Pub Date : 2024-09-10DOI: 10.1101/2024.09.05.611510
Alexander L Cope, Denizhan Pak, Michael A Gilchrist
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.
与转录和复制相比，mRNA 翻译过程既耗费能量，又容易出错。在 mRNA 翻译过程中，当核糖体在到达终止密码子之前脱离转录本时，就会发生无意义错误，导致能量投入到不完整且可能无功能的蛋白质中。无意义错误可能会给细胞带来巨大的能量负担，因此量化无意义错误的频率和能量成本至关重要。在这里，我们提出了一个核糖体运动模型，用于从高通量核糖体剖析数据中估算蛋白质的产生、延伸和无意义错误率。将该模型应用于 S. cerevisiae 中的一个核糖体剖析数据集，我们发现无义错误率在不同密码子之间存在差异，这与一般假设的有义密码子统一错误率相冲突。利用我们的参数估计，我们发现多种证据表明，针对无意义错误的选择是影响编码序列进化的主要力量，包括无意义错误给细胞带来的能量负担与核糖体暂停相当。我们的研究结果表明，应更多地考虑无义错误对编码序列进化的影响。
{"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}
Pub Date : 2024-09-10DOI: 10.1101/2024.09.10.612046
Alice May Godden, Benjamin Rix, Simone Immler
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.
背景：Piwi-interacting RNA（piRNA）是一种非编码小 RNA，可在转录后影响基因表达和调控。通过与转座元件（TE）的互补种子区结合，piRNA 保护基因组不被转座，因此需要一种工具将 piRNA 与互补的 TE 靶标联系起来。TEsmall等工具可以处理sRNA-seq数据集，生成差异表达的piRNA，为线虫开发的piRScan可以将piRNA与TE连接起来，但它要求用户知道感兴趣的目标区域并进行逆向研究。结果：因此，我们开发了 FishPi 来预测 piRNA 和 TE 之间的配对。FishPi 可处理单个 piRNA 或 fasta 格式的 piRNA 序列列表。该软件侧重于 piRNA:TE 种子区域，并分析 piRNA 互补性的参考 TE。对 TE 类型进行检查、计数并存储到字典中，同时记录基因组位点。任何 piRNA-TE 结合规则的更新都可以通过更新 FishPi 的底层代码轻松实现。FishPi 使用 tkinter 提供图形界面，用户只需输入 piRNA 序列，就能生成 piRNA:TE 动态的综合报告。FishPi 可以很容易地适用于其他基因组，为广大用户提供 piRNA 功能的解释。结论：用户将深入了解基因组年龄，FishPi 将帮助我们进一步了解 piRNA 的生物学作用及其与 TE 的相互作用，就像公共数据库改善了对小 RNA 作用的访问和了解一样。
{"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}
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.
{"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}
Pub Date : 2024-09-09DOI: 10.1101/2024.09.04.611329
Ostaizka Aizpurua, Amanda Bolt Botnen, Raphael Eisenhofer, Inaki Odriozola, Luisa Santos-Bay, Mads Bjorn Bjornsen, M Thomas P Gilbert, Antton Alberdi
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.
{"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}
Pub Date : 2024-09-09DOI: 10.1101/2024.09.08.611933
Jordan Douglas, Remco Bouckaert, Simon C Harris, Charles W Carter, Peter R Wills
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.
{"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}
Pub Date : 2024-09-09DOI: 10.1101/2024.09.06.611587
Tianyu Shen, Philippe Gadient, Justin Goodrich, Hannes Becher
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. To 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. Consistent 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. In 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.
{"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}
Pub Date : 2024-09-09DOI: 10.1101/2024.08.20.608864
Gianluca Merello, Montserrat Olivares-Costa, Lorenzo Basile, Tammy P. Pastor, Pablo Mendoza-Soto, Luis Padilla-Santiago, Gonzalo Mardones, Claudia Binda, Juan C. Opazo
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.
单胺氧化酶（MAO）基因家族编码执行单胺氧化脱氨的酶，这是降解去甲肾上腺素、血清素、多巴胺和其他胺类所需的过程。虽然哺乳动物的 MAO 酶（MAO A 和 MAO B）已被广泛研究，但其他家族成员的分子特性仅被部分揭示。本研究旨在探索单胺氧化酶的进化，重点是了解脊椎动物的 MAO 基因库。我们的分析表明，产生 MAO A 和 MAO B 的复制发生在距今 4.08 亿年至 3.52 亿年前的四足类动物祖先时期。非四足类有颌脊椎动物拥有 MAO A/B 的祖先前复制条件。我们的研究结果还在非四足有颌脊椎动物中发现了一个新的家族成员--MAO C。因此，大多数有颌脊椎动物都拥有两个 MAO 基因，即四足类的 MAO A 和 MAO B，以及非四足类有颌脊椎动物的 MAO A/B 和 MAO C，代表了不同的 MAO 基因谱系。无颌脊椎动物拥有单拷贝基因 MAO A/B/C。对印度-太平洋鲢鱼的MAO重组酶进行的酶学测定显示，MAO A/B和MAO C这两种蛋白质的酶学和分子特性与人类MAO A更为相似，前者的活性率明显高于所有其他MAO酶。我们的分析强调了扫描生命树寻找新基因系的重要性，以了解表型的多样性并详细了解它们的功能。
{"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}
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