Pub Date : 2024-09-18DOI: 10.1101/2024.09.13.612821
Yu Cheng, Filip Kolar, Roswitha Schmickl, Josselin Clo
It is broadly assumed that polyploidy success is due to an increase in fitness associated with whole genome duplication due to higher tolerance to stressful conditions. In agreement, several theoretical models found that, among other factors, a better tolerance to new environmental conditions can promote polyploidy establishment. These models, however, often made strong hypotheses, for example considering that diploids cannot adapt to new conditions, or that unreduced gametes production is not a limiting factor and that it is of a fixed quantity. In this paper, we challenged some of these hypotheses. We developed a theoretical model in which we modeled the joint evolution of a quantitative trait under selection and the production of unreduced gametes, this trait also being a quantitative trait; both traits were pleiotropically linked. We followed the adaptation of initially diploid populations to a new environment to which neo-tetraploid individuals were directly adapted. The generation of these autotetraploid individuals was enabled by the genetic production of unreduced gametes and by the environmental change modifying the average production of these gametes. We found that for realistic values of unreduced gametes production, adaptation to new environmental conditions was mainly achieved through adaptation of diploids to the new optimum rather than the fixation of newly adapted tetraploid individuals. In broader parameter sets, we found that the adaptation process led to mixed-ploidy populations, except when the populations were swamped with unreduced gametes, and that pleiotropy and environmental effects favored the co-existence of both cytotypes.
{"title":"How environment and genetic architecture of unreduced gametes shape the establishment of autopolyploids","authors":"Yu Cheng, Filip Kolar, Roswitha Schmickl, Josselin Clo","doi":"10.1101/2024.09.13.612821","DOIUrl":"https://doi.org/10.1101/2024.09.13.612821","url":null,"abstract":"It is broadly assumed that polyploidy success is due to an increase in fitness associated with whole genome duplication due to higher tolerance to stressful conditions. In agreement, several theoretical models found that, among other factors, a better tolerance to new environmental conditions can promote polyploidy establishment. These models, however, often made strong hypotheses, for example considering that diploids cannot adapt to new conditions, or that unreduced gametes production is not a limiting factor and that it is of a fixed quantity. In this paper, we challenged some of these hypotheses. We developed a theoretical model in which we modeled the joint evolution of a quantitative trait under selection and the production of unreduced gametes, this trait also being a quantitative trait; both traits were pleiotropically linked. We followed the adaptation of initially diploid populations to a new environment to which neo-tetraploid individuals were directly adapted. The generation of these autotetraploid individuals was enabled by the genetic production of unreduced gametes and by the environmental change modifying the average production of these gametes. We found that for realistic values of unreduced gametes production, adaptation to new environmental conditions was mainly achieved through adaptation of diploids to the new optimum rather than the fixation of newly adapted tetraploid individuals. In broader parameter sets, we found that the adaptation process led to mixed-ploidy populations, except when the populations were swamped with unreduced gametes, and that pleiotropy and environmental effects favored the co-existence of both cytotypes.","PeriodicalId":501183,"journal":{"name":"bioRxiv - Evolutionary Biology","volume":"19 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142264610","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 : 2024-09-17DOI: 10.1101/2024.09.12.612725
Diana Gamba, BromeCast Network, Jesse R Lasky
Local adaptation may facilitate range expansion during invasions, but the mechanisms promoting destructive invasions remain unclear. Cheatgrass (Bromus tectorum), native to Eurasia and Africa, has invaded globally, with particularly severe impacts in western North America. We sequenced 307 genotypes and conducted controlled experiments. We found that diverse lineages invaded North America, where long-distance gene flow is common. Ancestry and phenotypic clines in the native range predicted those in the invaded range, indicating pre-adapted genotypes colonized different regions. Common gardens showed directional selection on flowering time that reversed between warm and cold sites, potentially maintaining clines. In the Great Basin, genomic predictions of strong local adaptation identified sites where cheatgrass is most dominant. Preventing new introductions that may fuel adaptation is critical for managing ongoing invasions.
{"title":"Local adaptation to climate facilitates a global invasion","authors":"Diana Gamba, BromeCast Network, Jesse R Lasky","doi":"10.1101/2024.09.12.612725","DOIUrl":"https://doi.org/10.1101/2024.09.12.612725","url":null,"abstract":"Local adaptation may facilitate range expansion during invasions, but the mechanisms promoting destructive invasions remain unclear. Cheatgrass (Bromus tectorum), native to Eurasia and Africa, has invaded globally, with particularly severe impacts in western North America. We sequenced 307 genotypes and conducted controlled experiments. We found that diverse lineages invaded North America, where long-distance gene flow is common. Ancestry and phenotypic clines in the native range predicted those in the invaded range, indicating pre-adapted genotypes colonized different regions. Common gardens showed directional selection on flowering time that reversed between warm and cold sites, potentially maintaining clines. In the Great Basin, genomic predictions of strong local adaptation identified sites where cheatgrass is most dominant. Preventing new introductions that may fuel adaptation is critical for managing ongoing invasions.","PeriodicalId":501183,"journal":{"name":"bioRxiv - Evolutionary Biology","volume":"36 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142264559","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 : 2024-09-17DOI: 10.1101/2024.09.12.612586
Cammy H Beyts, Jonathan Wright, Yimen Araya-Ajoy, Kellie Watson
Maximising reproductive success is crucial to animal production systems, particularly in meeting global demands for animal products and improving commercially important traits. However, while social interactions and mating strategies are known to influence reproductive success in wild populations, their consideration in agricultural systems remains limited. Using an interdisciplinary framework that combines concepts from behavioural ecology and quantitative genetics in an animal breeding context, we investigated the role of sperm limitation and polygynous mating strategies (female polyandry, male monopolisation of females and male polygamy) in limiting female reproductive success in farmed Pekin ducks (Anas platyrthynchos domestica). We assessed the impact of these behaviours on chick production and quantified their genetic and environmental (co)variance. Our results revealed that the number of dam mates positively influenced chick production in female ducks. However, contrary to our expectation, skew in chick paternity (our measure of male monopolisation) was associated with increased female chick production, challenging the hypothesis that male monopolisation limits the sperm available to females and reduces their reproductive success. We found no evidence that male polygamy led to decreased female chick production. Genetic analysis revealed that female mate number and reproductive skew exhibit genetic variance, providing opportunities for targeted selection to enhance chick production. However, there was a negative genetic association between female polyandry and skew in chick paternity, suggesting a trade-off between these traits that would need to be considered in future selection programmes. Our findings highlight how concepts from behavioural ecology can be incorporated into breeding programmes, providing new opportunities to develop effective and sustainable breeding strategies.
{"title":"Towards explaining the fertility gap in farmed Pekin ducks","authors":"Cammy H Beyts, Jonathan Wright, Yimen Araya-Ajoy, Kellie Watson","doi":"10.1101/2024.09.12.612586","DOIUrl":"https://doi.org/10.1101/2024.09.12.612586","url":null,"abstract":"Maximising reproductive success is crucial to animal production systems, particularly in meeting global demands for animal products and improving commercially important traits. However, while social interactions and mating strategies are known to influence reproductive success in wild populations, their consideration in agricultural systems remains limited. Using an interdisciplinary framework that combines concepts from behavioural ecology and quantitative genetics in an animal breeding context, we investigated the role of sperm limitation and polygynous mating strategies (female polyandry, male monopolisation of females and male polygamy) in limiting female reproductive success in farmed Pekin ducks (Anas platyrthynchos domestica). We assessed the impact of these behaviours on chick production and quantified their genetic and environmental (co)variance. Our results revealed that the number of dam mates positively influenced chick production in female ducks. However, contrary to our expectation, skew in chick paternity (our measure of male monopolisation) was associated with increased female chick production, challenging the hypothesis that male monopolisation limits the sperm available to females and reduces their reproductive success. We found no evidence that male polygamy led to decreased female chick production. Genetic analysis revealed that female mate number and reproductive skew exhibit genetic variance, providing opportunities for targeted selection to enhance chick production. However, there was a negative genetic association between female polyandry and skew in chick paternity, suggesting a trade-off between these traits that would need to be considered in future selection programmes. Our findings highlight how concepts from behavioural ecology can be incorporated into breeding programmes, providing new opportunities to develop effective and sustainable breeding strategies.","PeriodicalId":501183,"journal":{"name":"bioRxiv - Evolutionary Biology","volume":"11 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142264560","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 : 2024-09-16DOI: 10.1101/2024.09.15.613132
Janna Lynn Fierst, Victoria K Eggers
Genome sequencing has revealed a tremendous diversity of transposable elements (TEs) in eukaryotes but there is little understanding of the evolutionary processes responsible for TE diversity. Non-autonomous TEs have lost the machinery necessary for transposition and rely on closely related autonomous TEs for critical proteins. We studied two mathematical models of TE regulation, one assuming that both autonomous tranposons and their non-autonomous relatives operate under the same regulatory logic, competing for transposition resources, and one assuming that autonomous TEs self-attenuate transposition while non-autonomous transposons continually increase, parasitizing their autonomous relatives. We implemented these models in stochastic simulations and studied how TE regulatory relationships influence transposons and populations. We found that only outcrossing populations evolving with Parasitic TE regulation resulted in stable maintenance of TEs. We tested our model predictions in Caenorhabditis genomes by annotating TEs in two focal families, autonomous LINEs and their non-autonomous SINE relatives and the DNA transposon Mutator. We found broad variation in autonomous - non-autonomous relationships and rapid mutational decay in the sequences that allow non-autonomous TEs to transpose. Together, our results suggest that individual TE families evolve according to disparate regulatory rules that are relevant in the early, acute stages of TE invasion.
基因组测序揭示了真核生物中转座元素（TE）的巨大多样性，但人们对造成转座元素多样性的进化过程却知之甚少。非自主TE失去了转座所需的机制，需要依赖密切相关的自主TE来获得关键蛋白。我们研究了两个关于TE调控的数学模型，一个假设自主转座子及其非自主近亲都在相同的调控逻辑下运行，竞争转座资源；另一个假设自主TE自我减弱转座，而非自主转座子不断增加，寄生于自主近亲。我们在随机模拟中实现了这些模型，并研究了TE调控关系如何影响转座子和种群。我们发现，只有在寄生性转座子调控下进化的外交种群才能稳定地维持转座子。我们在 Caenorhabditis 基因组中测试了我们的模型预测，对两个焦点家族中的 TE 进行了注释，这两个焦点家族是自主 LINE 及其非自主 SINE 亲缘基因和 DNA 转座子 Mutator。我们发现自主-非自主关系存在广泛差异，允许非自主TE进行转座的序列也存在快速突变衰减。总之，我们的研究结果表明，单个TE家族是根据不同的调控规则进化的，这些规则与TE入侵的早期、急性阶段相关。
{"title":"Regulatory logic and transposable element dynamics in nematode worm genomes","authors":"Janna Lynn Fierst, Victoria K Eggers","doi":"10.1101/2024.09.15.613132","DOIUrl":"https://doi.org/10.1101/2024.09.15.613132","url":null,"abstract":"Genome sequencing has revealed a tremendous diversity of transposable elements (TEs) in eukaryotes but there is little understanding of the evolutionary processes responsible for TE diversity. Non-autonomous TEs have lost the machinery necessary for transposition and rely on closely related autonomous TEs for critical proteins. We studied two mathematical models of TE regulation, one assuming that both autonomous tranposons and their non-autonomous relatives operate under the same regulatory logic, competing for transposition resources, and one assuming that autonomous TEs self-attenuate transposition while non-autonomous transposons continually increase, parasitizing their autonomous relatives. We implemented these models in stochastic simulations and studied how TE regulatory relationships influence transposons and populations. We found that only outcrossing populations evolving with Parasitic TE regulation resulted in stable maintenance of TEs. We tested our model predictions in Caenorhabditis genomes by annotating TEs in two focal families, autonomous LINEs and their non-autonomous SINE relatives and the DNA transposon Mutator. We found broad variation in autonomous - non-autonomous relationships and rapid mutational decay in the sequences that allow non-autonomous TEs to transpose. Together, our results suggest that individual TE families evolve according to disparate regulatory rules that are relevant in the early, acute stages of TE invasion.","PeriodicalId":501183,"journal":{"name":"bioRxiv - Evolutionary Biology","volume":"13 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142264561","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 : 2024-09-15DOI: 10.1101/2024.09.14.613021
Ali Akbari, Alison R. Barton, Steven Gazal, Zheng Li, Mohammadreza Kariminejad, Annabel Perry, Yating Zeng, Alissa Mittnik, Nick Patterson, Matthew Mah, Xiang Zhou, Alkes L. Price, Eric S. Lander, Ron Pinhasi, Nadin Rohland, Swapan Mallick, David Reich
We present a method for detecting evidence of natural selection in ancient DNA time-series data that leverages an opportunity not utilized in previous scans: testing for a consistent trend in allele frequency change over time. By applying this to 8433 West Eurasians who lived over the past 14000 years and 6510 contemporary people, we find an order of magnitude more genome-wide significant signals than previous studies: 347 independent loci with >99% probability of selection. Previous work showed that classic hard sweeps driving advantageous mutations to fixation have been rare over the broad span of human evolution, but in the last ten millennia, many hundreds of alleles have been affected by strong directional selection. Discoveries include an increase from ~0% to ~20% in 4000 years for the major risk factor for celiac disease at HLA-DQB1; a rise from ~0% to ~8% in 6000 years of blood type B; and fluctuating selection at the TYK2 tuberculosis risk allele rising from ~2% to ~9% from ~5500 to ~3000 years ago before dropping to ~3%. We identify instances of coordinated selection on alleles affecting the same trait, with the polygenic score today predictive of body fat percentage decreasing by around a standard deviation over ten millennia, consistent with the Thrifty Gene hypothesis that a genetic predisposition to store energy during food scarcity became disadvantageous after farming. We also identify selection for combinations of alleles that are today associated with lighter skin color, lower risk for schizophrenia and bipolar disease, slower health decline, and increased measures related to cognitive performance (scores on intelligence tests, household income, and years of schooling). These traits are measured in modern industrialized societies, so what phenotypes were adaptive in the past is unclear. We estimate selection coefficients at 9.9 million variants, enabling study of how Darwinian forces couple to allelic effects and shape the genetic architecture of complex traits.
{"title":"Pervasive findings of directional selection realize the promise of ancient DNA to elucidate human adaptation","authors":"Ali Akbari, Alison R. Barton, Steven Gazal, Zheng Li, Mohammadreza Kariminejad, Annabel Perry, Yating Zeng, Alissa Mittnik, Nick Patterson, Matthew Mah, Xiang Zhou, Alkes L. Price, Eric S. Lander, Ron Pinhasi, Nadin Rohland, Swapan Mallick, David Reich","doi":"10.1101/2024.09.14.613021","DOIUrl":"https://doi.org/10.1101/2024.09.14.613021","url":null,"abstract":"We present a method for detecting evidence of natural selection in ancient DNA time-series data that leverages an opportunity not utilized in previous scans: testing for a consistent trend in allele frequency change over time. By applying this to 8433 West Eurasians who lived over the past 14000 years and 6510 contemporary people, we find an order of magnitude more genome-wide significant signals than previous studies: 347 independent loci with >99% probability of selection. Previous work showed that classic hard sweeps driving advantageous mutations to fixation have been rare over the broad span of human evolution, but in the last ten millennia, many hundreds of alleles have been affected by strong directional selection. Discoveries include an increase from ~0% to ~20% in 4000 years for the major risk factor for celiac disease at HLA-DQB1; a rise from ~0% to ~8% in 6000 years of blood type B; and fluctuating selection at the TYK2 tuberculosis risk allele rising from ~2% to ~9% from ~5500 to ~3000 years ago before dropping to ~3%. We identify instances of coordinated selection on alleles affecting the same trait, with the polygenic score today predictive of body fat percentage decreasing by around a standard deviation over ten millennia, consistent with the <em>Thrifty Gene</em> hypothesis that a genetic predisposition to store energy during food scarcity became disadvantageous after farming. We also identify selection for combinations of alleles that are today associated with lighter skin color, lower risk for schizophrenia and bipolar disease, slower health decline, and increased measures related to cognitive performance (scores on intelligence tests, household income, and years of schooling). These traits are measured in modern industrialized societies, so what phenotypes were adaptive in the past is unclear. We estimate selection coefficients at 9.9 million variants, enabling study of how Darwinian forces couple to allelic effects and shape the genetic architecture of complex traits.","PeriodicalId":501183,"journal":{"name":"bioRxiv - Evolutionary Biology","volume":"37 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142264564","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 : 2024-09-15DOI: 10.1101/2024.09.14.613017
Benjamin H. Jenkins, Estelle S. Kilias, Fiona R. Savory, Megan E. S. Soerensen, Camille Poirier, Victoria Attah, Georgia C. Drew, Josephine Blagrave, Luis J. Galindo, Guy Leonard, Duncan D. Cameron, Michael A. Brockhurst, David S. Milner, Thomas A. Richards
Endosymbiosis was a key factor in the evolution of eukaryotic cellular complexity. Yet the mechanisms that allow host regulation of intracellular symbionts, a pre-requisite for stable endosymbiosis and subsequent organelle evolution, are largely unknown. Here, we describe an immune-like glycan-sensing/processing network, partly assembled through horizontal gene-transfers (HGTs), that enables Paramecium bursaria to control its green algal endosymbionts. Using phylogenetics, RNA-interference (RNAi), and metabolite exposure experiments, we show that P. bursaria regulates endosymbiont destruction using glycan-sensing/processing - a system that includes a eukaryotic-wide chitin-binding chitinase-like protein (CLP) localized to the host phago-lysosome. RNAi of CLP alters expression of eight host glycan-processing genes, including two prokaryote-derived HGTs, during endosymbiont destruction. Furthermore, glycan-sensing/processing dynamically regulates endosymbiont number in P. bursaria, plasticity crucial to maximize host fitness across ecological conditions. CLP is homologous to a human phagocyte-associated innate immune factor, revealing how immune functions can be alternatively adapted and expanded, partly through HGT, enabling endosymbiotic control.
{"title":"Immune-like glycan-sensing and horizontally-acquired glycan-processing orchestrate host control in a microbial endosymbiosis","authors":"Benjamin H. Jenkins, Estelle S. Kilias, Fiona R. Savory, Megan E. S. Soerensen, Camille Poirier, Victoria Attah, Georgia C. Drew, Josephine Blagrave, Luis J. Galindo, Guy Leonard, Duncan D. Cameron, Michael A. Brockhurst, David S. Milner, Thomas A. Richards","doi":"10.1101/2024.09.14.613017","DOIUrl":"https://doi.org/10.1101/2024.09.14.613017","url":null,"abstract":"Endosymbiosis was a key factor in the evolution of eukaryotic cellular complexity. Yet the mechanisms that allow host regulation of intracellular symbionts, a pre-requisite for stable endosymbiosis and subsequent organelle evolution, are largely unknown. Here, we describe an immune-like glycan-sensing/processing network, partly assembled through horizontal gene-transfers (HGTs), that enables Paramecium bursaria to control its green algal endosymbionts. Using phylogenetics, RNA-interference (RNAi), and metabolite exposure experiments, we show that P. bursaria regulates endosymbiont destruction using glycan-sensing/processing - a system that includes a eukaryotic-wide chitin-binding chitinase-like protein (CLP) localized to the host phago-lysosome. RNAi of CLP alters expression of eight host glycan-processing genes, including two prokaryote-derived HGTs, during endosymbiont destruction. Furthermore, glycan-sensing/processing dynamically regulates endosymbiont number in P. bursaria, plasticity crucial to maximize host fitness across ecological conditions. CLP is homologous to a human phagocyte-associated innate immune factor, revealing how immune functions can be alternatively adapted and expanded, partly through HGT, enabling endosymbiotic control.","PeriodicalId":501183,"journal":{"name":"bioRxiv - Evolutionary Biology","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142264563","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 : 2024-09-15DOI: 10.1101/2024.09.13.612959
Anne A Farrell, Camilla L Nesbo, Olga Zhaxybayeva
Evolutionary events leading to organismal preference for a specific growth temperature, as well as genes whose products are needed for a proper function at that temperature, are poorly understood. Using 64 bacteria from phylum Thermotogota as a model system, we examined how optimal growth temperature changed throughout Thermotogota history. We inferred that Thermotogota's last common ancestor was a thermophile and that some Thermotogota evolved the mesophilic and hyperthermophilic lifestyles secondarily. By modeling gain and loss of genes throughout Thermotogota history and by reconstructing their phylogenies, we demonstrated that adaptations to lower and higher growth temperature require both the acquisition of necessary genes and loss of unnecessary genes. Via a pangenome-wide association study, we correlated presence/absence of 68 gene families with specific optimal growth temperature intervals. While some of these genes are poorly characterized, most are involved in metabolism of amino acids, nucleotides, carbohydrates, and lipids, as well as in signal transduction and regulation of transcription. Most of the 68 genes have a history of horizontal gene transfer to/from other bacteria and archaea, suggesting that parallel acquisitions of genes likely promote independent adaptations of different Thermotogota species to specific growth temperatures.
{"title":"Bacterial growth temperature as a horizontally acquired polygenic trait","authors":"Anne A Farrell, Camilla L Nesbo, Olga Zhaxybayeva","doi":"10.1101/2024.09.13.612959","DOIUrl":"https://doi.org/10.1101/2024.09.13.612959","url":null,"abstract":"Evolutionary events leading to organismal preference for a specific growth temperature, as well as genes whose products are needed for a proper function at that temperature, are poorly understood. Using 64 bacteria from phylum Thermotogota as a model system, we examined how optimal growth temperature changed throughout Thermotogota history. We inferred that Thermotogota's last common ancestor was a thermophile and that some Thermotogota evolved the mesophilic and hyperthermophilic lifestyles secondarily. By modeling gain and loss of genes throughout Thermotogota history and by reconstructing their phylogenies, we demonstrated that adaptations to lower and higher growth temperature require both the acquisition of necessary genes and loss of unnecessary genes. Via a pangenome-wide association study, we correlated presence/absence of 68 gene families with specific optimal growth temperature intervals. While some of these genes are poorly characterized, most are involved in metabolism of amino acids, nucleotides, carbohydrates, and lipids, as well as in signal transduction and regulation of transcription. Most of the 68 genes have a history of horizontal gene transfer to/from other bacteria and archaea, suggesting that parallel acquisitions of genes likely promote independent adaptations of different Thermotogota species to specific growth temperatures.","PeriodicalId":501183,"journal":{"name":"bioRxiv - Evolutionary Biology","volume":"50 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142264562","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 : 2024-09-14DOI: 10.1101/2024.09.12.612246
Bharat Parthasarathy, Naeem Yusuf Shaikh, Sai Abhinay V, Varun Sai C, Sai Krishna MV, Krishna Kiran Vamsi Dasu
Increasing human interference has been shown to not only destroy habitats, but also alter the architecture of animal-built extended phenotypes. However, the impact of such architectural changes on the behaviour and survival of organisms remains poorly understood. To address this knowledge gap, we examined the impact of habitat modification using Indian social spider, Stegodyphus sarasinorum, as a model organism. S. sarasinorum colonies typically construct a three-dimensional (3D) capture web. Due to increasing habitat modification by humans, these spiders are now constrained to build two-dimensional (2D) capture webs adapting to man-made structures like fences. We investigated how these differing web architectures influence the collective behaviours and survival of S. sarasinorum. Our findings reveal that spiders with 2D capture webs emerged from their nests sooner, attacked prey faster, and had higher number of attacking spiders compared to those with 3D webs, suggesting 2D webs may be more efficient for hunting. However, despite their hunting advantages, spiders in 2D webs more frequently attacked the dangerous body parts of honeybees and were susceptible to honeybee stings. These results suggest that human-induced architectural modifications of the extended phenotype can have both benefits and costs for the organisms that built it. The survival benefits conferred by 3D capture webs against risky prey may have played a significant role in the evolutionary selection of this web architecture in S. sarasinorum.
{"title":"Extended Phenotype Influences Collective Behaviour and Survival in a Social Spider","authors":"Bharat Parthasarathy, Naeem Yusuf Shaikh, Sai Abhinay V, Varun Sai C, Sai Krishna MV, Krishna Kiran Vamsi Dasu","doi":"10.1101/2024.09.12.612246","DOIUrl":"https://doi.org/10.1101/2024.09.12.612246","url":null,"abstract":"Increasing human interference has been shown to not only destroy habitats, but also alter the architecture of animal-built extended phenotypes. However, the impact of such architectural changes on the behaviour and survival of organisms remains poorly understood. To address this knowledge gap, we examined the impact of habitat modification using Indian social spider, Stegodyphus sarasinorum, as a model organism. S. sarasinorum colonies typically construct a three-dimensional (3D) capture web. Due to increasing habitat modification by humans, these spiders are now constrained to build two-dimensional (2D) capture webs adapting to man-made structures like fences. We investigated how these differing web architectures influence the collective behaviours and survival of S. sarasinorum. Our findings reveal that spiders with 2D capture webs emerged from their nests sooner, attacked prey faster, and had higher number of attacking spiders compared to those with 3D webs, suggesting 2D webs may be more efficient for hunting. However, despite their hunting advantages, spiders in 2D webs more frequently attacked the dangerous body parts of honeybees and were susceptible to honeybee stings. These results suggest that human-induced architectural modifications of the extended phenotype can have both benefits and costs for the organisms that built it. The survival benefits conferred by 3D capture webs against risky prey may have played a significant role in the evolutionary selection of this web architecture in S. sarasinorum.","PeriodicalId":501183,"journal":{"name":"bioRxiv - Evolutionary Biology","volume":"32 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142264569","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 : 2024-09-14DOI: 10.1101/2024.09.12.612455
Ahmed M Hassan, Barbara Mühlemann, Tagreed L Al-Subhi, Jordi Rodon, Sherif A El-Kafrawy, Ziad Memish, Julia Melchert, Tobias Bleicker, Tiina Mauno, Stanley Perlman, Alimuddin Zumla, Terry C Jones, Marcel A Müller, Victor M Corman, Christian Drosten, Esam I Azhar
Middle East respiratory syndrome coronavirus (MERS-CoV) circulates in dromedary camels in the Arabian Peninsula and occasionally causes spillover infections in humans. Due to lack of sampling during the SARS-CoV-2 pandemic, current MERS-CoV diversity is poorly understood. Of 558 dromedary camel nasal swabs from Saudi Arabia, sampled November 2023 to January 2024, 39% were positive for MERS-CoV RNA by RT-PCR. We generated 42 MERS-CoV and seven human 229E-related CoV by high-throughput sequencing. For both viruses, the sequences fell into monophyletic clades apical to the most recent available genomes. The MERS-CoV sequences were most similar to those from lineage B5. The new MERS-CoVs sequences harbor unique genetic features, including novel amino acid polymorphisms in the Spike protein. The new variants require further phenotypic characterization to understand their impact. Ongoing MERS-CoV spillovers into humans pose significant public health concerns, emphasizing the need for continued surveillance and phenotypic studies.
{"title":"Ongoing evolution of Middle East Respiratory Syndrome Coronavirus, Kingdom of Saudi Arabia, 2023-2024","authors":"Ahmed M Hassan, Barbara Mühlemann, Tagreed L Al-Subhi, Jordi Rodon, Sherif A El-Kafrawy, Ziad Memish, Julia Melchert, Tobias Bleicker, Tiina Mauno, Stanley Perlman, Alimuddin Zumla, Terry C Jones, Marcel A Müller, Victor M Corman, Christian Drosten, Esam I Azhar","doi":"10.1101/2024.09.12.612455","DOIUrl":"https://doi.org/10.1101/2024.09.12.612455","url":null,"abstract":"Middle East respiratory syndrome coronavirus (MERS-CoV) circulates in dromedary camels in the Arabian Peninsula and occasionally causes spillover infections in humans. Due to lack of sampling during the SARS-CoV-2 pandemic, current MERS-CoV diversity is poorly understood. Of 558 dromedary camel nasal swabs from Saudi Arabia, sampled November 2023 to January 2024, 39% were positive for MERS-CoV RNA by RT-PCR. We generated 42 MERS-CoV and seven human 229E-related CoV by high-throughput sequencing. For both viruses, the sequences fell into monophyletic clades apical to the most recent available genomes. The MERS-CoV sequences were most similar to those from lineage B5. The new MERS-CoVs sequences harbor unique genetic features, including novel amino acid polymorphisms in the Spike protein. The new variants require further phenotypic characterization to understand their impact. Ongoing MERS-CoV spillovers into humans pose significant public health concerns, emphasizing the need for continued surveillance and phenotypic studies.","PeriodicalId":501183,"journal":{"name":"bioRxiv - Evolutionary Biology","volume":"199 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142269319","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 : 2024-09-14DOI: 10.1101/2024.09.12.612648
Lenka Caisova, Ewout Crombez, Minerva Susana Trejo Arellano, Marta Gut, Tyler Scott Alioto, Jessica Gomez-Garrido, Marc Dabad, Anna Esteve-Codina, Ivan Petrik, Ales Pencik, Ondrej Novak, Yves Van de Peer, Beatriz Vicoso, Jiri Friml
Green plants contain two algal lineages: Streptophyte algae that diverged into land plants and Chlorophyte algae that are mostly aquatic. Draparnaldia is a Chlorophyte alga morphologically resembling mosses and living in both, the aquatic and terrestrial habitats. Because of its complex morphology and terrestrial adaptations, Draparnaldia can provide new insights into the evolution of multicellularity and terrestrialization in green plants. To develop Draparnaldia into a model, we de novo sequenced its genome and transcriptomes, and profiled its phytohormone repertoire. We found that 1) Expanded gene families in Draparnaldia with respect to unicellular Chlamydomonas are linked to multicellularity and abiotic stresses. 2) Draparnaldias terrestrial adaptations are reflected at both the morphological and molecular levels. 3) Draparnaldia synthesizes most of the phytohormones used by land plants to thrive in terrestrial habitats. All of this makes Draparnaldia a powerful model to uncover and study alternative evolutionary trajectories towards multicellularity and terrestrialization in plants.
{"title":"The Draparnaldia genome: alternative mechanisms for multicellularity and terrestrialization in green plants","authors":"Lenka Caisova, Ewout Crombez, Minerva Susana Trejo Arellano, Marta Gut, Tyler Scott Alioto, Jessica Gomez-Garrido, Marc Dabad, Anna Esteve-Codina, Ivan Petrik, Ales Pencik, Ondrej Novak, Yves Van de Peer, Beatriz Vicoso, Jiri Friml","doi":"10.1101/2024.09.12.612648","DOIUrl":"https://doi.org/10.1101/2024.09.12.612648","url":null,"abstract":"Green plants contain two algal lineages: Streptophyte algae that diverged into land plants and Chlorophyte algae that are mostly aquatic. Draparnaldia is a Chlorophyte alga morphologically resembling mosses and living in both, the aquatic and terrestrial habitats. Because of its complex morphology and terrestrial adaptations, Draparnaldia can provide new insights into the evolution of multicellularity and terrestrialization in green plants. To develop Draparnaldia into a model, we de novo sequenced its genome and transcriptomes, and profiled its phytohormone repertoire. We found that 1) Expanded gene families in Draparnaldia with respect to unicellular Chlamydomonas are linked to multicellularity and abiotic stresses. 2) Draparnaldias terrestrial adaptations are reflected at both the morphological and molecular levels. 3) Draparnaldia synthesizes most of the phytohormones used by land plants to thrive in terrestrial habitats. All of this makes Draparnaldia a powerful model to uncover and study alternative evolutionary trajectories towards multicellularity and terrestrialization in plants.","PeriodicalId":501183,"journal":{"name":"bioRxiv - Evolutionary Biology","volume":"31 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142264567","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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