Pub Date : 2024-09-07DOI: 10.1101/2024.09.04.611149
Yan Wang, Hao Xu, Qinliu He, Zhiwei Wu, Zhen Gong, Guan-Zhu Han
Meiotic drivers are selfish genetic elements that distort fair segregation. The wtf genes are poison-antidote meiotic drivers that are experiencing rapid diversification in fission yeasts. However, gene duplication alone is insufficient to drive the diversification of wtf genes, given the poison encoded by a newly duplicated wtf gene can be detoxified by the antidote encoded by the original wtf gene. Here, we analyze the evolution of wtf genes across 21 strains of Schizosaccharomyces pombe. Knocking out each of 25 wtf genes in S. pombe strain 972h- separately does not attenuate the yeast growth, indicating that the wtf genes might be largely neutral to their carriers in asexual life cycle. Interestingly, wtf genes underwent recurrent and intricate recombination. As proof-of-principle, we generate a novel meiotic driver through artificial recombination between wtf drivers, and its encoded poison cannot be detoxified by the antidotes encoded by their parental wtf genes but can be detoxified by its own antidote. Therefore, we propose that recombination can generate new meiotic drivers and thus shape the diversification of the wtf drivers.
{"title":"Recombination shapes the diversification of the wtf meiotic drivers","authors":"Yan Wang, Hao Xu, Qinliu He, Zhiwei Wu, Zhen Gong, Guan-Zhu Han","doi":"10.1101/2024.09.04.611149","DOIUrl":"https://doi.org/10.1101/2024.09.04.611149","url":null,"abstract":"Meiotic drivers are selfish genetic elements that distort fair segregation. The wtf genes are poison-antidote meiotic drivers that are experiencing rapid diversification in fission yeasts. However, gene duplication alone is insufficient to drive the diversification of wtf genes, given the poison encoded by a newly duplicated wtf gene can be detoxified by the antidote encoded by the original wtf gene. Here, we analyze the evolution of wtf genes across 21 strains of Schizosaccharomyces pombe. Knocking out each of 25 wtf genes in S. pombe strain 972h- separately does not attenuate the yeast growth, indicating that the wtf genes might be largely neutral to their carriers in asexual life cycle. Interestingly, wtf genes underwent recurrent and intricate recombination. As proof-of-principle, we generate a novel meiotic driver through artificial recombination between wtf drivers, and its encoded poison cannot be detoxified by the antidotes encoded by their parental wtf genes but can be detoxified by its own antidote. Therefore, we propose that recombination can generate new meiotic drivers and thus shape the diversification of the wtf drivers.","PeriodicalId":501183,"journal":{"name":"bioRxiv - Evolutionary Biology","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142205474","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 : 2024-09-07DOI: 10.1101/2024.09.04.611202
Janet C Buckner, Katharine M Jack, Margaret Buehler, Amanda D Melin, Valerie AM Schoof, Eva Wikberg, Saul Chaves, Linda M Fedigan, Jessica W Lynch
The genes of the major histocompatibility complex (MHC) are vital to vertebrate immunity and may influence mate choice in several species. The extent to which the MHC influences female mate choice in primates remains poorly understood, and studies of MHC-based mate choice in platyrrhines are especially rare. White-faced capuchin monkeys (Cebus imitator) reside in multimale-multifemale groups where alpha males sire most of the offspring. In this study, we investigated the roles of social dominance, relatedness, and MHC genotypes in determining which mating pairs produced offspring in wild white-faced capuchins in the Sector Santa Rosa (SSR), Area de Conservacion Guanacaste, Costa Rica. We find that males in this population do not differ significantly in MHC metrics based on their social status or siring success. Using mixed conditional logit models and generalized linear models, we find that alpha males that are distantly related to reproducing females are significantly more likely to sire offspring while MHC metrics do not predict the probability of siring offspring, or becoming an alpha male. However, we do find some evidence that subordinate males heterozygous at MHC loci sire significantly more offspring than homozygous subordinates. Further, one-sided binomial simulations reveal that offspring are more frequently heterozygous at MHC loci than expected given the gene pool. We conclude that in this population with limited genomic variation, females may preferentially mate with MHC-diverse subordinate males when related to the alpha, leading to increased probabilities of MHC-diverse offspring.
{"title":"MHC heterozygosity may increase subordinate but not alpha male siring success in white-faced capuchin monkeys (Cebus imitator)","authors":"Janet C Buckner, Katharine M Jack, Margaret Buehler, Amanda D Melin, Valerie AM Schoof, Eva Wikberg, Saul Chaves, Linda M Fedigan, Jessica W Lynch","doi":"10.1101/2024.09.04.611202","DOIUrl":"https://doi.org/10.1101/2024.09.04.611202","url":null,"abstract":"The genes of the major histocompatibility complex (MHC) are vital to vertebrate immunity and may influence mate choice in several species. The extent to which the MHC influences female mate choice in primates remains poorly understood, and studies of MHC-based mate choice in platyrrhines are especially rare. White-faced capuchin monkeys (Cebus imitator) reside in multimale-multifemale groups where alpha males sire most of the offspring. In this study, we investigated the roles of social dominance, relatedness, and MHC genotypes in determining which mating pairs produced offspring in wild white-faced capuchins in the Sector Santa Rosa (SSR), Area de Conservacion Guanacaste, Costa Rica. We find that males in this population do not differ significantly in MHC metrics based on their social status or siring success. Using mixed conditional logit models and generalized linear models, we find that alpha males that are distantly related to reproducing females are significantly more likely to sire offspring while MHC metrics do not predict the probability of siring offspring, or becoming an alpha male. However, we do find some evidence that subordinate males heterozygous at MHC loci sire significantly more offspring than homozygous subordinates. Further, one-sided binomial simulations reveal that offspring are more frequently heterozygous at MHC loci than expected given the gene pool. We conclude that in this population with limited genomic variation, females may preferentially mate with MHC-diverse subordinate males when related to the alpha, leading to increased probabilities of MHC-diverse offspring.","PeriodicalId":501183,"journal":{"name":"bioRxiv - Evolutionary Biology","volume":"15 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142205473","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 : 2024-09-07DOI: 10.1101/2024.09.04.610786
Akanksha Singh, Markus G Stetter
Global climate change will impact worldwide crop yields, requiring shifts and adaptation of crop varieties. The recent global spread of crops across different continents shows how plants successfully colonized new environments. One such spread is the introduction of the nutritious pseudocereal amaranth to India. Grain amaranth has been domesticated over 6,000 years ago in three different regions of the Americas and was introduced to India approximately 500 years ago. Nowadays numerous local landraces grow throughout the country′s wide climatic conditions. We investigate the introduction of grain amaranth to India to understand the factors allowing successful establishment of crops to novel environments, using whole genome sequencing of almost 200 accessions from India and more than 100 accessions from the crop's native distribution. We find comparable levels of genetic diversity in the Americas and in India, despite the likely population bottleneck during the introduction to India. Surprisingly, the three grain amaranth species that were introduced do not show signs of gene-flow in India, while gene-flow in the Americas was high during the domestication of the crops. Correspondingly, the genetic differentiation between grain species was higher within India than in the native range, indicating a strong isolation between otherwise interbreeding populations. The reconstruction of the population history through demographic modelling of different scenarios suggested rapid expansion in the Indian population but a strong bottleneck in the native population, explaining the comparable diversity and isolation. We identified genomic loci under selection and associated with the climate in India that potentially enabled the adaptation to the new environment. These loci are predicted to provide an advantage under future climate scenarios, even in the native range. Our results suggest that introduced crops can act as reservoirs of genetic diversity, providing additional adaptive potential and resilience to future environmental change.
{"title":"Going New Places: Successful Adaptation and Genomic Integrity of Grain Amaranth in India","authors":"Akanksha Singh, Markus G Stetter","doi":"10.1101/2024.09.04.610786","DOIUrl":"https://doi.org/10.1101/2024.09.04.610786","url":null,"abstract":"Global climate change will impact worldwide crop yields, requiring shifts and adaptation of crop varieties. The recent global spread of crops across different continents shows how plants successfully colonized new environments. One such spread is the introduction of the nutritious pseudocereal amaranth to India. Grain amaranth has been domesticated over 6,000 years ago in three different regions of the Americas and was introduced to India approximately 500 years ago. Nowadays numerous local landraces grow throughout the country′s wide climatic conditions. We investigate the introduction of grain amaranth to India to understand the factors allowing successful establishment of crops to novel environments, using whole genome sequencing of almost 200 accessions from India and more than 100 accessions from the crop's native distribution. We find comparable levels of genetic diversity in the Americas and in India, despite the likely population bottleneck during the introduction to India. Surprisingly, the three grain amaranth species that were introduced do not show signs of gene-flow in India, while gene-flow in the Americas was high during the domestication of the crops. Correspondingly, the genetic differentiation between grain species was higher within India than in the native range, indicating a strong isolation between otherwise interbreeding populations. The reconstruction of the population history through demographic modelling of different scenarios suggested rapid expansion in the Indian population but a strong bottleneck in the native population, explaining the comparable diversity and isolation. We identified genomic loci under selection and associated with the climate in India that potentially enabled the adaptation to the new environment. These loci are predicted to provide an advantage under future climate scenarios, even in the native range. Our results suggest that introduced crops can act as reservoirs of genetic diversity, providing additional adaptive potential and resilience to future environmental change.","PeriodicalId":501183,"journal":{"name":"bioRxiv - Evolutionary Biology","volume":"95 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142205478","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 : 2024-09-07DOI: 10.1101/2024.09.03.611078
Timothy G Stephens, Julia Van Etten, Timothy McDermott, William Christian, Martha Chaverra, James Gurney, Yongsung Lee, Hocheol Kim, Chung Hyun Cho, Erik Chovancek, Philipp Westhoff, Antonia Otte, Trent R Northen, Benjamin P Bowen, Katherine B Louie, Kerrie Barry, Igor V Grigoriev, Thomas Mock, Shao-Lun Liu, Shin-ya Miyagishima, Masafumi Yoshinaga, Andreas Weber, Hwan Su Yoon, Debashish Bhattacharya
We investigated an alga-dominated geothermal spring community in Yellowstone National Park, USA. Our goal was to determine how cells cope with abiotic stressors during diurnal sampling that spanned over two orders of magnitude in solar irradiance. We report a community level response to toxic metal resistance and energy cycling that spans the three domains of life. Arsenic detoxification is accomplished via complementary gene expression by different lineages. Photosynthesis is dominated by Cyanidioschyzon, with the mixotroph, Galdieria, relegated to nighttime heterotrophy. Many key functions, including the cell cycle, are strongly regulated by diurnal light fluctuations. These results demonstrate that biotic interactions are highly structured in extreme habitats. We suggest this was also the case on the early Earth when geothermal springs were cradles of microbial life, prior to the origin of eukaryotes.
{"title":"Community-wide interactions sustain life in geothermal spring habitats","authors":"Timothy G Stephens, Julia Van Etten, Timothy McDermott, William Christian, Martha Chaverra, James Gurney, Yongsung Lee, Hocheol Kim, Chung Hyun Cho, Erik Chovancek, Philipp Westhoff, Antonia Otte, Trent R Northen, Benjamin P Bowen, Katherine B Louie, Kerrie Barry, Igor V Grigoriev, Thomas Mock, Shao-Lun Liu, Shin-ya Miyagishima, Masafumi Yoshinaga, Andreas Weber, Hwan Su Yoon, Debashish Bhattacharya","doi":"10.1101/2024.09.03.611078","DOIUrl":"https://doi.org/10.1101/2024.09.03.611078","url":null,"abstract":"We investigated an alga-dominated geothermal spring community in Yellowstone National Park, USA. Our goal was to determine how cells cope with abiotic stressors during diurnal sampling that spanned over two orders of magnitude in solar irradiance. We report a community level response to toxic metal resistance and energy cycling that spans the three domains of life. Arsenic detoxification is accomplished via complementary gene expression by different lineages. Photosynthesis is dominated by <em>Cyanidioschyzon</em>, with the mixotroph, <em>Galdieria</em>, relegated to nighttime heterotrophy. Many key functions, including the cell cycle, are strongly regulated by diurnal light fluctuations. These results demonstrate that biotic interactions are highly structured in extreme habitats. We suggest this was also the case on the early Earth when geothermal springs were cradles of microbial life, prior to the origin of eukaryotes.","PeriodicalId":501183,"journal":{"name":"bioRxiv - Evolutionary Biology","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142205475","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 : 2024-09-06DOI: 10.1101/2024.09.03.611027
Chew Chai, Jesse Gibson, Pengyang Li, Anusri Pampari, Aman Patel, Anshul Kundaje, Bo Wang
Cell types evolve into a hierarchy with related types grouped into families. How cell type diversification is constrained by the stable separation between families over vast evolutionary times remains unknown. Here, integrating single-nucleus multiomic sequencing and deep learning, we show that hundreds of sequence features (motifs) divide into distinct sets associated with accessible genomes of specific cell type families. This division is conserved across highly divergent, early-branching animals including flatworms and cnidarians. While specific interactions between motifs delineate cell type relationships within families, surprisingly, these interactions are not conserved between species. Consistently, while deep learning models trained on one species can predict accessibility of other species' sequences, their predictions frequently rely on distinct, but synonymous, motif combinations. We propose that long-term stability of cell type families is maintained through genome access specified by conserved motif sets, or 'vocabularies', whereas cell types diversify through flexible use of motifs within each set.
{"title":"Flexible use of conserved motif vocabularies constrains genome access in cell type evolution","authors":"Chew Chai, Jesse Gibson, Pengyang Li, Anusri Pampari, Aman Patel, Anshul Kundaje, Bo Wang","doi":"10.1101/2024.09.03.611027","DOIUrl":"https://doi.org/10.1101/2024.09.03.611027","url":null,"abstract":"Cell types evolve into a hierarchy with related types grouped into families. How cell type diversification is constrained by the stable separation between families over vast evolutionary times remains unknown. Here, integrating single-nucleus multiomic sequencing and deep learning, we show that hundreds of sequence features (motifs) divide into distinct sets associated with accessible genomes of specific cell type families. This division is conserved across highly divergent, early-branching animals including flatworms and cnidarians. While specific interactions between motifs delineate cell type relationships within families, surprisingly, these interactions are not conserved between species. Consistently, while deep learning models trained on one species can predict accessibility of other species' sequences, their predictions frequently rely on distinct, but synonymous, motif combinations. We propose that long-term stability of cell type families is maintained through genome access specified by conserved motif sets, or 'vocabularies', whereas cell types diversify through flexible use of motifs within each set.","PeriodicalId":501183,"journal":{"name":"bioRxiv - Evolutionary Biology","volume":"4 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142205308","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 : 2024-09-06DOI: 10.1101/2024.08.19.608647
Jeremy M Beaulieu, Brian C O'Meara
Nature is full of messy variation, which serves as the raw material for evolution. However, in comparative biology this variation is smoothed into averages. Overlooking this variation not only weakens our analyses but also risks selecting inaccurate models, generating false precision in parameter estimates, and creating artificial patterns. Furthermore, the complexity of uncertainty extends beyond traditional "measurement error," encompassing various sources of intraspecific variance. To address this, we propose the term "tip fog" to describe the variance between the true species mean and what is recorded, without implying a specific mechanism. We show why accounting for tip fog remains critical by showing its impact on continuous comparative models and discrete comparative and diversification models. We rederive methods to estimate this variance and use simulations to assess its feasibility and importance in a comparative context. Our findings reveal that ignoring tip fog substantially affects the accuracy of rate estimates, with higher tip fog levels showing greater biases from the true rates, as well as affecting which models are chosen. The findings underscore the importance of model selection and the potential consequences of neglecting tip fog, providing insights for improving the accuracy of comparative methods in evolutionary biology.
{"title":"Navigating \"tip fog\": Embracing uncertainty in tip measurements","authors":"Jeremy M Beaulieu, Brian C O'Meara","doi":"10.1101/2024.08.19.608647","DOIUrl":"https://doi.org/10.1101/2024.08.19.608647","url":null,"abstract":"Nature is full of messy variation, which serves as the raw material for evolution. However, in comparative biology this variation is smoothed into averages. Overlooking this variation not only weakens our analyses but also risks selecting inaccurate models, generating false precision in parameter estimates, and creating artificial patterns. Furthermore, the complexity of uncertainty extends beyond traditional \"measurement error,\" encompassing various sources of intraspecific variance. To address this, we propose the term \"tip fog\" to describe the variance between the true species mean and what is recorded, without implying a specific mechanism. We show why accounting for tip fog remains critical by showing its impact on continuous comparative models and discrete comparative and diversification models. We rederive methods to estimate this variance and use simulations to assess its feasibility and importance in a comparative context. Our findings reveal that ignoring tip fog substantially affects the accuracy of rate estimates, with higher tip fog levels showing greater biases from the true rates, as well as affecting which models are chosen. The findings underscore the importance of model selection and the potential consequences of neglecting tip fog, providing insights for improving the accuracy of comparative methods in evolutionary biology.","PeriodicalId":501183,"journal":{"name":"bioRxiv - Evolutionary Biology","volume":"63 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142205477","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 : 2024-09-06DOI: 10.1101/2024.09.02.610914
Keita Saito, Masahito Tsuboi, Yuma Takahashi
Variation enables short-term evolution (microevolution), but its role in long-term evolution (macroevolution) is debated. Here, we analyzed a dataset of Drosophila wing variation across six levels of biological organization to demonstrate that microevolutionary variation and macroevolutionary divergence are positively correlated at all levels from variation within an individual to 40 million years of macroevolution. Surprisingly, the strongest relationship was between developmental noise and macroevolutionary divergence-levels thought to be the most distant-whereas the relationship between standing genetic variation and population divergence was modest, despite established theoretical predictions. Our results indicate that the congruence of developmental system with long-term history of fluctuation in adaptive peaks creates dialectical relationships between microevolution and macroevolution.
{"title":"Conserved variation across scales unveils dialectical relationships of micro- and macroevolution","authors":"Keita Saito, Masahito Tsuboi, Yuma Takahashi","doi":"10.1101/2024.09.02.610914","DOIUrl":"https://doi.org/10.1101/2024.09.02.610914","url":null,"abstract":"Variation enables short-term evolution (microevolution), but its role in long-term evolution (macroevolution) is debated. Here, we analyzed a dataset of Drosophila wing variation across six levels of biological organization to demonstrate that microevolutionary variation and macroevolutionary divergence are positively correlated at all levels from variation within an individual to 40 million years of macroevolution. Surprisingly, the strongest relationship was between developmental noise and macroevolutionary divergence-levels thought to be the most distant-whereas the relationship between standing genetic variation and population divergence was modest, despite established theoretical predictions. Our results indicate that the congruence of developmental system with long-term history of fluctuation in adaptive peaks creates dialectical relationships between microevolution and macroevolution.","PeriodicalId":501183,"journal":{"name":"bioRxiv - Evolutionary Biology","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142205480","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 : 2024-09-05DOI: 10.1101/2024.09.05.611523
Djivan Prentout, Daria Bykova, Carla R Hoge, Daniel M Hooper, Callum S McDiarmid, Felix Wu, Simon Griffith, Marc de Manuel, Molly Przeworski
Most of our understanding of the fundamental processes of mutation and recombination stems from a handful of disparate model organisms and pedigree studies of mammals, with little known about other vertebrates. To gain a broader comparative perspective, we focused on the zebra finch (Taeniopygia castanotis), which, like other birds, differs from mammals in its karyotype (which includes many micro-chromosomes), in the mechanism by which recombination is directed to the genome, and in aspects of ontogenesis. We collected genome sequences from three generation pedigrees that provide information about 80 meioses, inferring 202 single-point de novo mutations, 1,174 crossovers, and 275 non-crossovers. On that basis, we estimated a sex averaged mutation rate of 5.0 x 10-9 per base pair per generation, on par with mammals that have a similar generation time. Also as in mammals, we found a paternal germline mutation bias at later stages of gametogenesis (of 1.7 to 1) but no discernible difference between sexes in early development. We also examined recombination patterns, and found that the sex-averaged crossover rate on macro-chromosomes (1.05 cM/Mb) is again similar to values observed in mammals, as is the spatial distribution of crossovers, with a pronounced enrichment near telomeres. In contrast, non-crossover rates are more uniformly distributed. On micro-chromosomes, sex-averaged crossover rates are substantially higher (4.21 cM/Mb), as expected from crossover homeostasis, and both crossover and non-crossover events are more uniformly distributed. At a finer scale, recombination events overlap CpG islands more often than expected by chance, as expected in the absence of PRDM9. Despite differences in the mechanism by which recombination events are specified and the presence of many micro-chromosomes, estimates of the degree of GC-biased gene conversion (59%), the mean non-crossover conversion tract length (~23 bp), and the non-crossover to crossover ratio (6.7:1) are all comparable to those reported in primates and mice. The conservation of mutation and recombination properties from zebra finch to mammals suggest that these processes have evolved under stabilizing selection.
{"title":"Conservation of mutation and recombination parameters between mammals and zebra finch","authors":"Djivan Prentout, Daria Bykova, Carla R Hoge, Daniel M Hooper, Callum S McDiarmid, Felix Wu, Simon Griffith, Marc de Manuel, Molly Przeworski","doi":"10.1101/2024.09.05.611523","DOIUrl":"https://doi.org/10.1101/2024.09.05.611523","url":null,"abstract":"Most of our understanding of the fundamental processes of mutation and recombination stems from a handful of disparate model organisms and pedigree studies of mammals, with little known about other vertebrates. To gain a broader comparative perspective, we focused on the zebra finch (Taeniopygia castanotis), which, like other birds, differs from mammals in its karyotype (which includes many micro-chromosomes), in the mechanism by which recombination is directed to the genome, and in aspects of ontogenesis. We collected genome sequences from three generation pedigrees that provide information about 80 meioses, inferring 202 single-point de novo mutations, 1,174 crossovers, and 275 non-crossovers. On that basis, we estimated a sex averaged mutation rate of 5.0 x 10-9 per base pair per generation, on par with mammals that have a similar generation time. Also as in mammals, we found a paternal germline mutation bias at later stages of gametogenesis (of 1.7 to 1) but no discernible difference between sexes in early development. We also examined recombination patterns, and found that the sex-averaged crossover rate on macro-chromosomes (1.05 cM/Mb) is again similar to values observed in mammals, as is the spatial distribution of crossovers, with a pronounced enrichment near telomeres. In contrast, non-crossover rates are more uniformly distributed. On micro-chromosomes, sex-averaged crossover rates are substantially higher (4.21 cM/Mb), as expected from crossover homeostasis, and both crossover and non-crossover events are more uniformly distributed. At a finer scale, recombination events overlap CpG islands more often than expected by chance, as expected in the absence of PRDM9. Despite differences in the mechanism by which recombination events are specified and the presence of many micro-chromosomes, estimates of the degree of GC-biased gene conversion (59%), the mean non-crossover conversion tract length (~23 bp), and the non-crossover to crossover ratio (6.7:1) are all comparable to those reported in primates and mice. The conservation of mutation and recombination properties from zebra finch to mammals suggest that these processes have evolved under stabilizing selection.","PeriodicalId":501183,"journal":{"name":"bioRxiv - Evolutionary Biology","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142205479","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 : 2024-09-05DOI: 10.1101/2024.09.04.611237
Kelsey Williamson, Laura Eme, Hector Baños, Charley McCarthy, Edward Susko, Ryoma Kamikawa, Russell J.S. Orr, Sergio A. Muñoz-Gómez, Alastair G.B. Simpson, Andrew J. Roger
The eukaryote Tree of Life (eToL) depicts the relationships among all eukaryotic organisms; its root represents the last eukaryotic common ancestor (LECA) from which all extant complex lifeforms are descended. Locating this root is crucial for reconstructing the features of LECA, both as the endpoint of eukaryogenesis and the start-point for evolution of the myriad complex traits underpinning the diversification of living eukaryotes. However, the position of the root remains contentious due to pervasive phylogenetic artefacts stemming from inadequate evolutionary models, poor taxon sampling, and limited phylogenetic signal. Here, we estimate the root of the eToL with unprecedented resolution based on a new, much larger, dataset of mitochondrial proteins which includes all known eukaryotic supergroups. Our comprehensive analyses with state-of-the-art phylogenetic models reveal that the eukaryotic root lies between two multi-supergroup assemblages: "Opimoda+" and "Diphoda+". Compellingly, this position is consistently supported across different models and robustness analyses. Notably, groups containing "typical excavates" are placed on both sides of the root, suggesting the complex features of the "excavate" cell architecture trace back to LECA. This study is the most comprehensive phylogenetic investigation of the eukaryote root to date, shedding light on the ancestral cells from which extant eukaryotes arose and providing a crucial framework for investigating the origin and evolution of canonical eukaryotic features.
{"title":"A robustly rooted tree of eukaryotes reveals their excavate ancestry.","authors":"Kelsey Williamson, Laura Eme, Hector Baños, Charley McCarthy, Edward Susko, Ryoma Kamikawa, Russell J.S. Orr, Sergio A. Muñoz-Gómez, Alastair G.B. Simpson, Andrew J. Roger","doi":"10.1101/2024.09.04.611237","DOIUrl":"https://doi.org/10.1101/2024.09.04.611237","url":null,"abstract":"The eukaryote Tree of Life (eToL) depicts the relationships among all eukaryotic organisms; its root represents the last eukaryotic common ancestor (LECA) from which all extant complex lifeforms are descended. Locating this root is crucial for reconstructing the features of LECA, both as the endpoint of eukaryogenesis and the start-point for evolution of the myriad complex traits underpinning the diversification of living eukaryotes. However, the position of the root remains contentious due to pervasive phylogenetic artefacts stemming from inadequate evolutionary models, poor taxon sampling, and limited phylogenetic signal. Here, we estimate the root of the eToL with unprecedented resolution based on a new, much larger, dataset of mitochondrial proteins which includes all known eukaryotic supergroups. Our comprehensive analyses with state-of-the-art phylogenetic models reveal that the eukaryotic root lies between two multi-supergroup assemblages: \"Opimoda+\" and \"Diphoda+\". Compellingly, this position is consistently supported across different models and robustness analyses. Notably, groups containing \"typical excavates\" are placed on both sides of the root, suggesting the complex features of the \"excavate\" cell architecture trace back to LECA. This study is the most comprehensive phylogenetic investigation of the eukaryote root to date, shedding light on the ancestral cells from which extant eukaryotes arose and providing a crucial framework for investigating the origin and evolution of canonical eukaryotic features.","PeriodicalId":501183,"journal":{"name":"bioRxiv - Evolutionary Biology","volume":"65 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142205483","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 : 2024-09-05DOI: 10.1101/2024.09.05.611396
Berra Erkosar, Cindy Dupuis, Loriane Savary, Tadeusz J. Kawecki
Shared developmental, physiological and molecular mechanisms can generate strong genetic covariances across suites of traits, constraining genetic variability and evolvability to certain axes in multivariate trait space ("variational modules" or "syndromes"). Such trait suites will not only respond jointly to selection; they will also covary across populations that diverged from one another by genetic drift. We report evidence for such a genetically correlated trait suite in Drosophila melanogaster. It links high expression of glycolysis and TCA cycle genes, high abundance of mitochondria and high spontaneous locomotor activity with low degree of adiposity, and low endurance and early death under starvation. This "power-endurance" axis is also aligned with abundance of certain metabolites, notably low trehalose (blood sugar) and high levels of some amino acids and their derivatives, including creatine, a compound known to facilitate energy production in muscles. Our evidence comes from six replicate "Selected" populations adapted to a nutrient-poor larval diet regime during 250 generations of experimental evolution and six "Control" populations evolved in parallel on a standard diet regime. We found that, within each of these experimental evolutionary regime, the above traits strongly covaried along the power-endurance axis across replicate populations which diversified by drift, indicating a shared genetic architecture. The two evolutionary regimes also drove divergence along this axis, with Selected populations on average displaced towards the "power" direction compared to Controls. Aspects of this "power-endurance" axis resemble the "pace of life" syndrome and the "thrifty phenotype"; it may have evolved as part of a coordinated organismal response to nutritional conditions.
{"title":"Shared genetic architecture links energy metabolism, behavior and starvation resistance along a power-endurance axis","authors":"Berra Erkosar, Cindy Dupuis, Loriane Savary, Tadeusz J. Kawecki","doi":"10.1101/2024.09.05.611396","DOIUrl":"https://doi.org/10.1101/2024.09.05.611396","url":null,"abstract":"Shared developmental, physiological and molecular mechanisms can generate strong genetic covariances across suites of traits, constraining genetic variability and evolvability to certain axes in multivariate trait space (\"variational modules\" or \"syndromes\"). Such trait suites will not only respond jointly to selection; they will also covary across populations that diverged from one another by genetic drift. We report evidence for such a genetically correlated trait suite in Drosophila melanogaster. It links high expression of glycolysis and TCA cycle genes, high abundance of mitochondria and high spontaneous locomotor activity with low degree of adiposity, and low endurance and early death under starvation. This \"power-endurance\" axis is also aligned with abundance of certain metabolites, notably low trehalose (blood sugar) and high levels of some amino acids and their derivatives, including creatine, a compound known to facilitate energy production in muscles. Our evidence comes from six replicate \"Selected\" populations adapted to a nutrient-poor larval diet regime during 250 generations of experimental evolution and six \"Control\" populations evolved in parallel on a standard diet regime. We found that, within each of these experimental evolutionary regime, the above traits strongly covaried along the power-endurance axis across replicate populations which diversified by drift, indicating a shared genetic architecture. The two evolutionary regimes also drove divergence along this axis, with Selected populations on average displaced towards the \"power\" direction compared to Controls. Aspects of this \"power-endurance\" axis resemble the \"pace of life\" syndrome and the \"thrifty phenotype\"; it may have evolved as part of a coordinated organismal response to nutritional conditions.","PeriodicalId":501183,"journal":{"name":"bioRxiv - Evolutionary Biology","volume":"66 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142205482","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}
京公网安备 11010802042870号
京ICP备2023020795号-1
扫码关注我们
求助内容：
应助结果提醒方式：