Molecular biology and evolution最新文献

筛选
英文 中文
Recurrent Duplication and Diversification of a Vital DNA Repair Gene Family Across Drosophila. 果蝇中一个重要 DNA 修复基因家族的重复和多样化。
IF 11 1区 生物学
Molecular biology and evolution Pub Date : 2024-06-01 DOI: 10.1093/molbev/msae113
Cara L Brand, Genevieve T Oliver, Isabella Z Farkas, Michael Buszczak, Mia T Levine
{"title":"Recurrent Duplication and Diversification of a Vital DNA Repair Gene Family Across Drosophila.","authors":"Cara L Brand, Genevieve T Oliver, Isabella Z Farkas, Michael Buszczak, Mia T Levine","doi":"10.1093/molbev/msae113","DOIUrl":"10.1093/molbev/msae113","url":null,"abstract":"<p><p>Maintaining genome integrity is vital for organismal survival and reproduction. Essential, broadly conserved DNA repair pathways actively preserve genome integrity. However, many DNA repair proteins evolve adaptively. Ecological forces like UV exposure are classically cited drivers of DNA repair evolution. Intrinsic forces like repetitive DNA, which also imperil genome integrity, have received less attention. We recently reported that a Drosophila melanogaster-specific DNA satellite array triggered species-specific, adaptive evolution of a DNA repair protein called Spartan/MH. The Spartan family of proteases cleave hazardous, covalent crosslinks that form between DNA and proteins (\"DNA-protein crosslink repair\"). Appreciating that DNA satellites are both ubiquitous and universally fast-evolving, we hypothesized that satellite DNA turnover spurs adaptive evolution of DNA-protein crosslink repair beyond a single gene and beyond the D. melanogaster lineage. This hypothesis predicts pervasive Spartan gene family diversification across Drosophila species. To study the evolutionary history of the Drosophila Spartan gene family, we conducted population genetic, molecular evolution, phylogenomic, and tissue-specific expression analyses. We uncovered widespread signals of positive selection across multiple Spartan family genes and across multiple evolutionary timescales. We also detected recurrent Spartan family gene duplication, divergence, and gene loss. Finally, we found that ovary-enriched parent genes consistently birthed functionally diverged, testis-enriched daughter genes. To account for Spartan family diversification, we introduce a novel mechanistic model of antagonistic coevolution that links DNA satellite evolution and adaptive regulation of Spartan protease activity. This framework promises to accelerate our understanding of how DNA repeats drive recurrent evolutionary innovation to preserve genome integrity.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":null,"pages":null},"PeriodicalIF":11.0,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11210505/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141311079","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Signatures of Adaptation and Purifying Selection in Highland Populations of Dasiphora fruticosa. Dasiphora fruticosa高原种群的适应和净化选择特征。
IF 11 1区 生物学
Molecular biology and evolution Pub Date : 2024-06-01 DOI: 10.1093/molbev/msae099
Fu-Sheng Yang, Min Liu, Xing Guo, Chao Xu, Juan Jiang, Weixue Mu, Dongming Fang, Yong-Chao Xu, Fu-Min Zhang, Ying-Hui Wang, Ting Yang, Hongyun Chen, Sunil Kumar Sahu, Ruirui Li, Guanlong Wang, Qiang Wang, Xun Xu, Song Ge, Huan Liu, Ya-Long Guo
{"title":"Signatures of Adaptation and Purifying Selection in Highland Populations of Dasiphora fruticosa.","authors":"Fu-Sheng Yang, Min Liu, Xing Guo, Chao Xu, Juan Jiang, Weixue Mu, Dongming Fang, Yong-Chao Xu, Fu-Min Zhang, Ying-Hui Wang, Ting Yang, Hongyun Chen, Sunil Kumar Sahu, Ruirui Li, Guanlong Wang, Qiang Wang, Xun Xu, Song Ge, Huan Liu, Ya-Long Guo","doi":"10.1093/molbev/msae099","DOIUrl":"10.1093/molbev/msae099","url":null,"abstract":"<p><p>High mountains harbor a considerable proportion of biodiversity, but we know little about how diverse plants adapt to the harsh environment. Here we finished a high-quality genome assembly for Dasiphora fruticosa, an ecologically important plant distributed in the Qinghai-Tibetan Plateau and lowland of the Northern Hemisphere, and resequenced 592 natural individuals to address how this horticulture plant adapts to highland. Demographic analysis revealed D. fruticosa underwent a bottleneck after Naynayxungla Glaciation. Selective sweep analysis of two pairs of lowland and highland populations identified 63 shared genes related to cell wall organization or biogenesis, cellular component organization, and dwarfism, suggesting parallel adaptation to highland habitats. Most importantly, we found that stronger purging of estimated genetic load due to inbreeding in highland populations apparently contributed to their adaptation to the highest mountain. Our results revealed how plants could tolerate the extreme plateau, which could provide potential insights for species conservation and crop breeding.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":null,"pages":null},"PeriodicalIF":11.0,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11156201/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141071440","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Diversity and Molecular Evolution of Nonvisual Opsin Genes across Environmental, Developmental, and Morphological Adaptations in Frogs. 蛙类非视觉蛋白基因在环境、发育和形态适应方面的多样性和分子进化。
IF 11 1区 生物学
Molecular biology and evolution Pub Date : 2024-06-01 DOI: 10.1093/molbev/msae090
John L Boyette, Rayna C Bell, Matthew K Fujita, Kate N Thomas, Jeffrey W Streicher, David J Gower, Ryan K Schott
{"title":"Diversity and Molecular Evolution of Nonvisual Opsin Genes across Environmental, Developmental, and Morphological Adaptations in Frogs.","authors":"John L Boyette, Rayna C Bell, Matthew K Fujita, Kate N Thomas, Jeffrey W Streicher, David J Gower, Ryan K Schott","doi":"10.1093/molbev/msae090","DOIUrl":"10.1093/molbev/msae090","url":null,"abstract":"<p><p>Nonvisual opsins are transmembrane proteins expressed in the eyes and other tissues of many animals. When paired with a light-sensitive chromophore, nonvisual opsins form photopigments involved in various nonvisual, light-detection functions including circadian rhythm regulation, light-seeking behaviors, and seasonal responses. Here, we investigate the molecular evolution of nonvisual opsin genes in anuran amphibians (frogs and toads). We test several evolutionary hypotheses including the predicted loss of nonvisual opsins due to nocturnal ancestry and potential functional differences in nonvisual opsins resulting from environmental light variation across diverse anuran ecologies. Using whole-eye transcriptomes of 81 species, combined with genomes, multitissue transcriptomes, and independently annotated genes from an additional 21 species, we identify which nonvisual opsins are present in anuran genomes and those that are also expressed in the eyes, compare selective constraint among genes, and test for potential adaptive evolution by comparing selection between discrete ecological classes. At the genomic level, we recovered all 18 ancestral vertebrate nonvisual opsins, indicating that anurans demonstrate the lowest documented amount of opsin gene loss among ancestrally nocturnal tetrapods. We consistently found expression of 14 nonvisual opsins in anuran eyes and detected positive selection in a subset of these genes. We also found shifts in selective constraint acting on nonvisual opsins in frogs with differing activity periods, habitats, distributions, life histories, and pupil shapes, which may reflect functional adaptation. Although many nonvisual opsins remain poorly understood, these findings provide insight into the diversity and evolution of these genes across anurans, filling an important gap in our understanding of vertebrate opsins and setting the stage for future research on their functional evolution across taxa.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":null,"pages":null},"PeriodicalIF":11.0,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11181710/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140912455","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Severe Bottleneck Impacted the Genomic Structure of Egg-Eating Cichlids in Lake Victoria. 维多利亚湖食卵慈鲷的基因组结构受到严重瓶颈影响
IF 11 1区 生物学
Molecular biology and evolution Pub Date : 2024-06-01 DOI: 10.1093/molbev/msae093
Minami Imamoto, Haruna Nakamura, Mitsuto Aibara, Ryo Hatashima, Ismael A Kimirei, Benedicto B Kashindye, Takehiko Itoh, Masato Nikaido
{"title":"Severe Bottleneck Impacted the Genomic Structure of Egg-Eating Cichlids in Lake Victoria.","authors":"Minami Imamoto, Haruna Nakamura, Mitsuto Aibara, Ryo Hatashima, Ismael A Kimirei, Benedicto B Kashindye, Takehiko Itoh, Masato Nikaido","doi":"10.1093/molbev/msae093","DOIUrl":"10.1093/molbev/msae093","url":null,"abstract":"<p><p>Within 15,000 years, the explosive adaptive radiation of haplochromine cichlids in Lake Victoria, East Africa, generated 500 endemic species. In the 1980s, the upsurge of Nile perch, a carnivorous fish artificially introduced to the lake, drove the extinction of more than 200 endemic cichlids. The Nile perch predation particularly harmed piscivorous cichlids, including paedophages, cichlids eat eggs and fries, which is an example of the unique trophic adaptation seen in African cichlids. Here, aiming to investigate past demographic events possibly triggered by the invasion of Nile perch and the subsequent impacts on the genetic structure of cichlids, we conducted large-scale comparative genomics. We discovered evidence of recent bottleneck events in 4 species, including 2 paedophages, which began during the 1970s to 1980s, and population size rebounded during the 1990s to 2000s. The timing of the bottleneck corresponded to the historical records of endemic haplochromines\" disappearance and later resurgence, which is likely associated with the introduction of Nile perch by commercial demand to Lake Victoria in the 1950s. Interestingly, among the 4 species that likely experienced bottleneck, Haplochromis sp. \"matumbi hunter,\" a paedophagous cichlid, showed the most severe bottleneck signatures. The components of shared ancestry inferred by ADMIXTURE suggested a high genetic differentiation between matumbi hunter and other species. In contrast, our phylogenetic analyses highly supported the monophyly of the 5 paedophages, consistent with the results of previous studies. We conclude that high genetic differentiation of matumbi hunter occurred due to the loss of shared genetic components among haplochromines in Lake Victoria caused by the recent severe bottleneck.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":null,"pages":null},"PeriodicalIF":11.0,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11166178/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141086955","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Measuring the Efficiency of Purging by non-random Mating in Human Populations. 衡量人类种群中通过非随机交配进行净化的效率。
IF 11 1区 生物学
Molecular biology and evolution Pub Date : 2024-06-01 DOI: 10.1093/molbev/msae094
Romain Laurent, Laure Gineau, José Utge, Sophie Lafosse, Chan Leakhena Phoeung, Tatyana Hegay, Robert Olaso, Anne Boland, Jean-François Deleuze, Bruno Toupance, Evelyne Heyer, Anne-Louise Leutenegger, Raphaëlle Chaix
{"title":"Measuring the Efficiency of Purging by non-random Mating in Human Populations.","authors":"Romain Laurent, Laure Gineau, José Utge, Sophie Lafosse, Chan Leakhena Phoeung, Tatyana Hegay, Robert Olaso, Anne Boland, Jean-François Deleuze, Bruno Toupance, Evelyne Heyer, Anne-Louise Leutenegger, Raphaëlle Chaix","doi":"10.1093/molbev/msae094","DOIUrl":"10.1093/molbev/msae094","url":null,"abstract":"<p><p>Human populations harbor a high concentration of deleterious genetic variants. Here, we tested the hypothesis that non-random mating practices affect the distribution of these variants, through exposure in the homozygous state, leading to their purging from the population gene pool. To do so, we produced whole-genome sequencing data for two pairs of Asian populations exhibiting different alliance rules and rates of inbreeding, but with similar effective population sizes. The results show that populations with higher rates of inbred matings do not purge deleterious variants more efficiently. Purging therefore has a low efficiency in human populations, and different mating practices lead to a similar mutational load.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":null,"pages":null},"PeriodicalIF":11.0,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11184347/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141261994","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Boundary Effects Cause False Signals of Range Expansions in Population Genomic Data. 边界效应会导致种群基因组数据中出现范围扩大的错误信号。
IF 11 1区 生物学
Molecular biology and evolution Pub Date : 2024-05-03 DOI: 10.1093/molbev/msae091
Petri Kemppainen, Rhiannon Schembri, Paolo Momigliano
{"title":"Boundary Effects Cause False Signals of Range Expansions in Population Genomic Data.","authors":"Petri Kemppainen, Rhiannon Schembri, Paolo Momigliano","doi":"10.1093/molbev/msae091","DOIUrl":"10.1093/molbev/msae091","url":null,"abstract":"<p><p>Studying range expansions is central for understanding genetic variation through space and time as well as for identifying refugia and biological invasions. Range expansions are characterized by serial founder events causing clines of decreasing genetic diversity away from the center of origin and asymmetries in the two-dimensional allele frequency spectra. These asymmetries, summarized by the directionality index (ψ), are sensitive to range expansions and persist for longer than clines in genetic diversity. In continuous and finite meta-populations, genetic drift tends to be stronger at the edges of the species distribution in equilibrium populations and populations undergoing range expansions alike. Such boundary effects are expected to affect geographic patterns in genetic diversity and ψ. Here we demonstrate that boundary effects cause high false positive rates in equilibrium meta-populations when testing for range expansions. In the simulations, the absolute value of ψ (|ψ|) in equilibrium data sets was proportional to the fixation index (FST). By fitting signatures of range expansions as a function of ɛ |ψ|/FST and geographic clines in ψ, strong evidence for range expansions could be detected in data from a recent rapid invasion of the cane toad, Rhinella marina, in Australia, but not in 28 previously published empirical data sets from Australian scincid lizards that were significant for the standard range expansion tests. Thus, while clinal variation in ψ is still the most sensitive statistic to range expansions, to detect true signatures of range expansions in natural populations, its magnitude needs to be considered in relation to the overall levels of genetic structuring in the data.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":null,"pages":null},"PeriodicalIF":11.0,"publicationDate":"2024-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11135943/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140920976","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Dating Ammonia-Oxidizing Bacteria with Abundant Eukaryotic Fossils. 用丰富的真核生物化石确定氨氧化细菌的年代。
IF 10.7 1区 生物学
Molecular biology and evolution Pub Date : 2024-05-03 DOI: 10.1093/molbev/msae096
Tianhua Liao, Sishuo Wang, Hao Zhang, Eva E Stüeken, Haiwei Luo
{"title":"Dating Ammonia-Oxidizing Bacteria with Abundant Eukaryotic Fossils.","authors":"Tianhua Liao, Sishuo Wang, Hao Zhang, Eva E Stüeken, Haiwei Luo","doi":"10.1093/molbev/msae096","DOIUrl":"10.1093/molbev/msae096","url":null,"abstract":"<p><p>Evolution of a complete nitrogen (N) cycle relies on the onset of ammonia oxidation, which aerobically converts ammonia to nitrogen oxides. However, accurate estimation of the antiquity of ammonia-oxidizing bacteria (AOB) remains challenging because AOB-specific fossils are absent and bacterial fossils amenable to calibrate molecular clocks are rare. Leveraging the ancient endosymbiosis of mitochondria and plastid, as well as using state-of-the-art Bayesian sequential dating approach, we obtained a timeline of AOB evolution calibrated largely by eukaryotic fossils. We show that the first AOB evolved in marine Gammaproteobacteria (Gamma-AOB) and emerged between 2.1 and 1.9 billion years ago (Ga), thus postdating the Great Oxidation Event (GOE; 2.4 to 2.32 Ga). To reconcile the sedimentary N isotopic signatures of ammonia oxidation occurring near the GOE, we propose that ammonia oxidation likely occurred at the common ancestor of Gamma-AOB and Gammaproteobacterial methanotrophs, or the actinobacterial/verrucomicrobial methanotrophs which are known to have ammonia oxidation activities. It is also likely that nitrite was transported from the terrestrial habitats where ammonia oxidation by archaea took place. Further, we show that the Gamma-AOB predated the anaerobic ammonia-oxidizing (anammox) bacteria, implying that the emergence of anammox was constrained by the availability of dedicated ammonia oxidizers which produce nitrite to fuel anammox. Our work supports a new hypothesis that N redox cycle involving nitrogen oxides evolved rather late in the ocean.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":null,"pages":null},"PeriodicalIF":10.7,"publicationDate":"2024-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11135946/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141081983","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Unpredictability of the Fitness Effects of Antimicrobial Resistance Mutations Across Environments in Escherichia coli. 大肠杆菌抗菌药耐药性突变在不同环境下的适应性效应的不可预测性。
IF 10.7 1区 生物学
Molecular biology and evolution Pub Date : 2024-05-03 DOI: 10.1093/molbev/msae086
Aaron Hinz, André Amado, Rees Kassen, Claudia Bank, Alex Wong
{"title":"Unpredictability of the Fitness Effects of Antimicrobial Resistance Mutations Across Environments in Escherichia coli.","authors":"Aaron Hinz, André Amado, Rees Kassen, Claudia Bank, Alex Wong","doi":"10.1093/molbev/msae086","DOIUrl":"10.1093/molbev/msae086","url":null,"abstract":"<p><p>The evolution of antimicrobial resistance (AMR) in bacteria is a major public health concern, and antibiotic restriction is often implemented to reduce the spread of resistance. These measures rely on the existence of deleterious fitness effects (i.e. costs) imposed by AMR mutations during growth in the absence of antibiotics. According to this assumption, resistant strains will be outcompeted by susceptible strains that do not pay the cost during the period of restriction. The fitness effects of AMR mutations are generally studied in laboratory reference strains grown in standard growth environments; however, the genetic and environmental context can influence the magnitude and direction of a mutation's fitness effects. In this study, we measure how three sources of variation impact the fitness effects of Escherichia coli AMR mutations: the type of resistance mutation, the genetic background of the host, and the growth environment. We demonstrate that while AMR mutations are generally costly in antibiotic-free environments, their fitness effects vary widely and depend on complex interactions between the mutation, genetic background, and environment. We test the ability of the Rough Mount Fuji fitness landscape model to reproduce the empirical data in simulation. We identify model parameters that reasonably capture the variation in fitness effects due to genetic variation. However, the model fails to accommodate the observed variation when considering multiple growth environments. Overall, this study reveals a wealth of variation in the fitness effects of resistance mutations owing to genetic background and environmental conditions, which will ultimately impact their persistence in natural populations.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":null,"pages":null},"PeriodicalIF":10.7,"publicationDate":"2024-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11110942/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140867684","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Wiring Between Close Nodes in Molecular Networks Evolves More Quickly Than Between Distant Nodes. 分子网络中近距离节点之间的连接比远距离节点之间的连接发展得更快。
IF 10.7 1区 生物学
Molecular biology and evolution Pub Date : 2024-05-03 DOI: 10.1093/molbev/msae098
Alejandro Gil-Gomez, Joshua S Rest
{"title":"Wiring Between Close Nodes in Molecular Networks Evolves More Quickly Than Between Distant Nodes.","authors":"Alejandro Gil-Gomez, Joshua S Rest","doi":"10.1093/molbev/msae098","DOIUrl":"10.1093/molbev/msae098","url":null,"abstract":"<p><p>As species diverge, a wide range of evolutionary processes lead to changes in protein-protein interaction (PPI) networks and metabolic networks. The rate at which molecular networks evolve is an important question in evolutionary biology. Previous empirical work has focused on interactomes from model organisms to calculate rewiring rates, but this is limited by the relatively small number of species and sparse nature of network data across species. We present a proxy for variation in network topology: variation in drug-drug interactions (DDIs), obtained by studying drug combinations (DCs) across taxa. Here, we propose the rate at which DDIs change across species as an estimate of the rate at which the underlying molecular network changes as species diverge. We computed the evolutionary rates of DDIs using previously published data from a high-throughput study in gram-negative bacteria. Using phylogenetic comparative methods, we found that DDIs diverge rapidly over short evolutionary time periods, but that divergence saturates over longer time periods. In parallel, we mapped drugs with known targets in PPI and cofunctional networks. We found that the targets of synergistic DDIs are closer in these networks than other types of DCs and that synergistic interactions have a higher evolutionary rate, meaning that nodes that are closer evolve at a faster rate. Future studies of network evolution may use DC data to gain larger-scale perspectives on the details of network evolution within and between species.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":null,"pages":null},"PeriodicalIF":10.7,"publicationDate":"2024-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11136681/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141071511","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Genetic Causes and Genomic Consequences of Breakdown of Distyly in Linum trigynum. 三尖杉(Linum trigynum)淀粉分解的遗传原因和基因组后果。
IF 10.7 1区 生物学
Molecular biology and evolution Pub Date : 2024-05-03 DOI: 10.1093/molbev/msae087
Juanita Gutiérrez-Valencia, Panagiotis-Ioannis Zervakis, Zoé Postel, Marco Fracassetti, Aleksandra Losvik, Sara Mehrabi, Ignas Bunikis, Lucile Soler, P William Hughes, Aurélie Désamoré, Benjamin Laenen, Mohamed Abdelaziz, Olga Vinnere Pettersson, Juan Arroyo, Tanja Slotte
{"title":"Genetic Causes and Genomic Consequences of Breakdown of Distyly in Linum trigynum.","authors":"Juanita Gutiérrez-Valencia, Panagiotis-Ioannis Zervakis, Zoé Postel, Marco Fracassetti, Aleksandra Losvik, Sara Mehrabi, Ignas Bunikis, Lucile Soler, P William Hughes, Aurélie Désamoré, Benjamin Laenen, Mohamed Abdelaziz, Olga Vinnere Pettersson, Juan Arroyo, Tanja Slotte","doi":"10.1093/molbev/msae087","DOIUrl":"10.1093/molbev/msae087","url":null,"abstract":"<p><p>Distyly is an iconic floral polymorphism governed by a supergene, which promotes efficient pollen transfer and outcrossing through reciprocal differences in the position of sexual organs in flowers, often coupled with heteromorphic self-incompatibility. Distyly has evolved convergently in multiple flowering plant lineages, but has also broken down repeatedly, often resulting in homostylous, self-compatible populations with elevated rates of self-fertilization. Here, we aimed to study the genetic causes and genomic consequences of the shift to homostyly in Linum trigynum, which is closely related to distylous Linum tenue. Building on a high-quality genome assembly, we show that L. trigynum harbors a genomic region homologous to the dominant haplotype of the distyly supergene conferring long stamens and short styles in L. tenue, suggesting that loss of distyly first occurred in a short-styled individual. In contrast to homostylous Primula and Fagopyrum, L. trigynum harbors no fixed loss-of-function mutations in coding sequences of S-linked distyly candidate genes. Instead, floral gene expression analyses and controlled crosses suggest that mutations downregulating the S-linked LtWDR-44 candidate gene for male self-incompatibility and/or anther height could underlie homostyly and self-compatibility in L. trigynum. Population genomic analyses of 224 whole-genome sequences further demonstrate that L. trigynum is highly self-fertilizing, exhibits significantly lower genetic diversity genome-wide, and is experiencing relaxed purifying selection and less frequent positive selection on nonsynonymous mutations relative to L. tenue. Our analyses shed light on the loss of distyly in L. trigynum, and advance our understanding of a common evolutionary transition in flowering plants.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":null,"pages":null},"PeriodicalIF":10.7,"publicationDate":"2024-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11114476/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140864571","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
相关产品
×
本文献相关产品
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信