Genome Biology and Evolution最新文献

{"title":"From macro to micro: De novo genomes of Aedes mosquitoes enable comparative genomics among close and distant relatives.","authors":"Gen Morinaga, Darío Balcazar, Athanase Badolo, Diana Iyaloo, Luciano Tantely, Theo Mouillaud, Maria Sharakhova, Scott M Geib, Christophe Paupy, Diego Ayala, Jeffrey R Powell, Andrea Gloria-Soria, John Soghigian","doi":"10.1093/gbe/evaf142","DOIUrl":"10.1093/gbe/evaf142","url":null,"abstract":"<p><p>The yellow fever mosquito (Aedes aegypti) is an organism of high medical importance because it is the primary vector for diseases such as yellow fever, Zika, dengue, and chikungunya. Its medical importance has made it a subject of numerous efforts to understand their biology. One such effort, was the development of a high-quality reference genome (AaegL5). However, this reference genome was sourced from a highly inbred laboratory strain with unknown geographic origin. Thus, the reference is not representative of a wild mosquito, let alone one from its native range in sub-Saharan Africa. To better understand the genetic architecture of Ae. aegypti and their sister species, we developed two de novo chromosome-scale genomes with sequences sourced from single individuals: one of Ae. aegypti formosus (Aaf) from Burkina Faso and one of Ae. mascarensis (Am) from Mauritius. Both genomes exhibit high contiguity and gene completeness, comparable to AaegL5. While Aaf exhibits high degree of synteny to AaegL5, it also exhibits several large inversions. We also conducted comparative genomic analyses using our genomes and other publicly available culicid reference genomes to find extensive chromosomal rearrangements between major lineages. The expanded gene families common to Aaf, AaegL5, and Am revealed that while the overarching category of genes that have expanded are similar, the specific genes that have expanded differ. Our findings elucidate novel insights into chromosome evolution at both microevolutionary and macroevolutionary scales. The genomic resources we present are additions to a growing arsenal for biologists in understanding mosquito biology and genome evolution.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144617240","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evolution of dosage-sensitive genes by tissue-restricted expression changes.","authors":"Alan M Rice, Yuanshuo Li, Pauric Donnelly, Aoife McLysaght","doi":"10.1093/gbe/evaf132","DOIUrl":"https://doi.org/10.1093/gbe/evaf132","url":null,"abstract":"<p><p>Dosage-sensitive genes have characteristic patterns of evolution that include being refractory to small-scale duplication, depleted on human benign copy number variants (CNVs) and enriched on pathogenic CNVs. This intolerance to copy number change is likely due to an expression constraint that exists in one or more tissues. While genomic copy number changes alter the encompassed genes' expression across all tissues, expression quantitative trait loci (eQTLs) -genomic regions harbouring sequence variants that influence the expression level of one or more genes- can act in a tissue-specific manner. In this work we examine expression variation of presumed dosage-sensitive and non-dosage-sensitive genes to discover how the locus duplicability constraints translate into gene expression constraints. Here we test the hypothesis that expression changes due to the presence of eQTLs acting in unconstrained tissues will not be deleterious and thus allow dosage-sensitive genes to vary expression while obeying constraints in other tissues. Using eQTLs across 48 human tissues from The Genotype-Tissue Expression (GTEx) project, we find that dosage-sensitive genes are enriched for being affected by eQTLs and that the eQTLs affecting dosage-sensitive genes are biased towards having narrow tissue-specificity with these genes having fewer eQTL-affected tissues than non-dosage-sensitive genes. Additionally, we find that dosage-sensitive genes are depleted for being affected by broad tissue breadth eQTLs, likely due to the increased chance of these eQTLs conflicting with expression constraints and being removed by purifying selection. These patterns suggest that the dosage-sensitivity that shapes the evolution of these genes by precluding copy number evolution also restricts their evolutionary trajectories to changes in expression regulation compatible with their functional constraints. Thus deeper interpretation of the patterns of constraints can be informative of the temporal or spatial location of the gene dosage sensitivity and contribute to our understanding of functional genomics.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144575352","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sexual Antagonism and Sex Determination in Three Syngnathid Species Alongside a Male Pregnancy Gradient.","authors":"Arseny Dubin, Jamie Parker, Astrid Böhne, Olivia Roth","doi":"10.1093/gbe/evaf103","DOIUrl":"10.1093/gbe/evaf103","url":null,"abstract":"<p><p>The allocation of energy toward gamete production, parental care, mate choice, and secondary sexual signals fosters divergence in selection between the sexes, giving rise to opposing fitness strategies and sexual antagonism. The shared genetic makeup results in single genomic loci that harbor a gene or variant with varying fitness impacts on each sex. The resolution of this intralocus sexual conflict relies on intersex bias in gene expression and/or the formation of sex-linked genomic regions, which may also play a role in regulating sex determination. Shifts in the sex determination locus may happen. While the precise mechanisms driving these shifts are unknown, sexual antagonism was long believed to be a major contributor. To investigate the link between sexual antagonism and sex determination, we selected three syngnathid species along the gradient of their unique male pregnancy that evolved with different intensities of precopulatory sexual selection, i.e. sex-specific roles in mate choice. Examining intersex genetic divergence (Fst) and patterns of sex-biased expression, we revealed that precopulatory sexual selection and male pregnancy, rather than male pregnancy alone, are the primary drivers of sexual antagonism. In addition, we identified processes involving noncoding RNAs and biased variant expression as mediators of sexual antagonism. Notably, we discovered an intraspecies sex chromosome polymorphism in the seahorse Hippocampus erectus. The polymorphism may have resulted from generations of captive breeding or represents a natural polymorphism in wild populations. Our findings suggest that sexual antagonism resolution mechanisms can directly shape sex determination evolution across species, providing key insights into the molecular pathways underlying reproductive adaptation and diversification.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":"17 7","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12229468/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144575354","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Divergence and Selection in a Cryptic Species Complex (Geonoma undata: Arecaceae) in the Northern Andes of Colombia.","authors":"Carmen P Webster, Margot Paris, Ingrid Olivares, Martin F Wojciechowski, Michael Kessler, María José Sanín","doi":"10.1093/gbe/evaf130","DOIUrl":"10.1093/gbe/evaf130","url":null,"abstract":"<p><p>Palms (family Arecaceae) are integral to understanding the evolution of tropical rainforests due to their long evolutionary history, high species richness, and hyper dominance in these ecosystems. Some palm genera, like Geonoma, are regionally and locally species-rich and abundant in Neotropical rainforests, but factors contributing to their divergence and ultimately their diversification remain poorly explored. A recent phylogenomic study identified the Geonoma undata complex, with high levels of genetic distinctiveness of different geographically proximal groups, describing it as a hyper-cryptic radiation. Here, we seek to disentangle the factors that contribute to genetic divergence in the G. undata cryptic species complex in the Northern Colombian Andes, where various forms ascribable to different taxonomic, morphological, and genetic groups exist. To address this, we pursued three main aims using nuclear single nucleotide polymorphisms distributed along over 4,000 genomic regions from 156 individuals. (i) We identified populations and used diversity metrics to understand evolutionary scenarios across pairwise comparisons of those populations. Geographically sympatric populations display evidence for allopatric selection that is likely explained by elevational segregation. (ii) Tajima's D was used to infer broad genomic trends in selection and drift. In general, divergence between populations is enhanced by drift through population expansions. (iii) Lastly, we used outlier divergence and selection statistics to identify genes with outstanding divergence under significant positive selection. Two genes were identified that fit this description and are found to play functional roles in phenology, such as light response and flowering time.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":"17 7","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12279445/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144682459","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Distribution and Evolutionary Trajectories of β-Lactamases in Vibrio: Genomic Insights from Carbenicillin-Hydrolyzing Class A β-Lactamases (CARB) in the Harveyi and Cholerae Clades.","authors":"Yaofan Yang, Xingkun Jin, Zhe Zhao","doi":"10.1093/gbe/evaf128","DOIUrl":"10.1093/gbe/evaf128","url":null,"abstract":"<p><p>Antibiotic resistance mediated by β-lactamases, encoded by bla genes, is a significant global health threat, necessitating systematic studies of their diversity and evolution, particularly among pathogenic bacteria lineages. Leveraging over 6,000 quality-filtered Vibrio genomes alongside six newly sequenced marine symbiotic strains representing 128 nominal and 57 unclassified Vibrio species, our study extends taxonomic breadth and resolution for investigating β-lactamase diversity. We identified 4,431 β-lactamases across 41 species, encompassing all four Ambler classes (A-D). Among these, carbenicillin-hydrolyzing Class A β-lactamases encoded by blaCARB family were the most prevalent (60.7%) and exhibited a clade-centric distribution particularly in Harveyi clade and V. cholerae, underscoring the influence of specific ecological and evolutionary pressures. We refined carbenicillin-hydrolyzing Class A β-lactamase classification into two subfamilies: CARB-17-like (blaCARB-17-like) confined to Harveyi clade and CARB-1-like (blaCARB-1-like) found exclusively outside Harveyi clade based on phylogenetic placement, sequence similarity, and inheritance patterns, providing a clearer framework for delineating their functional and phylogenetic nuances. Notably, blaCARB-17-like genes in nonpathogenic Harveyi Subclade II showed significantly relaxed selection, accompanied by unusual mutations within key conserved motifs especially catalytic serine residues, suggesting evolutionary drift that may compromise canonical enzymatic activity. Furthermore, blaCARB-17-like genes, present as a single copy, emerged as a core gene in Harveyi clade, showing promise as a diagnostic marker for clinically significant Harveyi clade species, despite limited yet significant interspecies genetic exchanges mediated by recombination or mobile genetic elements. Our study advances the understanding of β-lactamase evolution and genomic distribution in Vibrio, with broad implications for diagnostic applications and resistance management strategies.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12269762/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144484144","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evolution of the Nonvisual and Visual Opsin Gene Repertoire in Ray-Finned Fishes.","authors":"Maxime Policarpo, Lily G Fogg, Fabio Cortesi, Walter Salzburger","doi":"10.1093/gbe/evaf129","DOIUrl":"10.1093/gbe/evaf129","url":null,"abstract":"<p><p>Photoreception-the detection of light for image formation (vision) as well as for nonimage-forming purposes (circadian regulation and DNA repair)-is critical to the survival of most animals. In vertebrates, photoreception is mediated by opsin proteins, which are classified, according to their function, into visual and nonvisual opsins. Here, we provide the most comprehensive study to date on the evolution of the opsin gene family in the largest class of vertebrates, actinopterygians, with a particular focus on the understudied nonvisual opsins. Based on an in-depth analysis of 535 high-quality genomes, we document great variation in gene numbers in the different opsin gene subfamilies across ray-finned fishes and show that visual opsins are more prone to duplications and losses than nonvisual opsins. We provide evidence that visual and nonvisual opsins coevolve in ray-finned fishes, both in terms of copy numbers and selective pressures acting on their coding sequences, probably in response to the different photic environments they inhabit. Species that live in dim light or in the dark (such as in caves or the deep sea) had reduced visual and nonvisual opsin gene repertoires, while polar species feature accelerated evolution in both. Fishes that rely on electroreception show a slight reduction in the number of visual and nonvisual opsin genes and accelerated evolution of the remaining genes. We further found that genes of the phototransduction cascade coevolve with opsins. Finally, the finding that nonvisual opsins are mainly expressed in the testes and ovaries (after the eyes) supports a function in gamete biology.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12279438/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144505544","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"On Rooting and Dating Viral Trees With a Changing Evolutionary Rate Following Host-Switching.","authors":"Xuhua Xia","doi":"10.1093/gbe/evaf134","DOIUrl":"10.1093/gbe/evaf134","url":null,"abstract":"<p><p>Viral host-switching from host H1 to host H2 is often associated with changes in viral evolutionary rate r. The pre-switching rate r1 in H1 may stay the same or increase/decrease to a new rate r2 in H2 during the host-switching and host-adapting process, depending on the difference between H1 and H2. The changing rate has previously been modeled by a linear function when the time interval is short but is better modeled by a sigmoidal function. The author presents the mathematical model, illustrates its application, and implements the rooting and dating methods in a new version of the user-friendly TRAD program, which is freely available at https://dambe.bio.uottawa.ca/TRAD/TRAD.aspx. Application of the method to a phylogeny of early SARS-CoV-2 genomes revealed (i) an increase in r in late February 2020 contributed mainly by the D614G lineage, (ii) a significantly better fit of the sigmoidal-rate model to the SARS-CoV-2 evolution than the constant-rate model, and (iii) the common ancestor of the included SARS-CoV-2 genomes dated to November 20, 2019.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12284395/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144575353","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chromosomal Inversions and Their Potential Impact on the Evolution of Arboviral Vector Aedes aegypti.","authors":"Jiangtao Liang, Noah H Rose, Ilya I Brusentsov, Varvara Lukyanchikova, Dmitriy A Karagodin, Yifan Feng, Andrey A Yurchenko, Atashi Sharma, Massamba Sylla, Joel Lutomiah, Athanase Badolo, Ogechukwu Aribodor, Cassandra Gonzalez Acosta, Barry Wilmer Alto, Nazni Wasi Ahmad, Elina M Baricheva, Zhijian Tu, Diego Ayala, Andrea Gloria-Soria, William C Black, Jeffrey R Powell, Igor V Sharakhov, Carolyn S McBride, Maria V Sharakhova","doi":"10.1093/gbe/evaf118","DOIUrl":"10.1093/gbe/evaf118","url":null,"abstract":"<p><p>Chromosomal inversions play a crucial role in evolution and have been found to regulate epidemiologically significant traits in malaria mosquitoes. However, they have not been characterized in Aedes aegypti, the primary vector of arboviruses, due to the poor structure of its polytene chromosomes. The Hi-C proximity ligation approach was used to identify chromosomal inversions in 25 strains of A. aegypti obtained from its worldwide distribution and in one strain of Aedes mascarensis. The study identified 21 multimegabase polymorphic inversions ranging in size from 5 to 55 Mbp. Inversions were more abundant in African than in non-African strains, 15 versus 3 inversions, with the highest number observed in West Africa. All inversions were grouped into two geographic clusters of African or non-African origin, suggesting their association with A. aegypti subspecies. Inversions were unevenly distributed along chromosomal arms, with the highest number found in the 1q and 3p arms homologous to the inversion-rich 2R chromosomal arm in the malaria vector Anopheles gambiae. Direct comparison of inversions between A. aegypti and An. gambiae revealed significant overlap in their genomic locations. This finding may explain the parallel evolution of the two species under similar environmental conditions. Some of the inversions colocalized with chemoreceptor genes and quantitative trait loci associated with pathogen infection, suggesting their potential role in host preference and disease transmission. Our study revealed the large pool of structural variations in the A. aegypti genome and provides the foundation for future studies of their impact on the biology of this important arboviral vector.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12242385/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144505543","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Positive Selection of a Starch Synthesis Gene and Phenotypic Differentiation of Starch Accumulation in Symbiotic and Free-Living Coral Symbiont Dinoflagellate Species.","authors":"Yuu Ishii, Shunsuke Kanamori, Ryusaku Deguchi, Masakado Kawata, Shinichiro Maruyama, Takashi Yoshida, Ryoma Kamikawa","doi":"10.1093/gbe/evaf133","DOIUrl":"10.1093/gbe/evaf133","url":null,"abstract":"<p><p>Symbiosis is a basis for species diversification through interactions between organisms. In tropical and subtropical oceans, dinoflagellate symbionts belonging to the family Symbiodiniaceae, including the genus Symbiodinium, support the flourishment of cnidarian hosts, including corals, and thereby the ecology of oligotrophic oceans through their photosynthate carbon transfers. Although the genus Symbiodinium includes both free-living and symbiotic species, the detailed genetic background of their lifestyle differences remains unclear. In this study, we identified candidate genes involved in the evolutionary acquisition or maintenance of symbiosis in Symbiodinium spp. by detecting genes that have undergone positive selection during symbiotic and free-living lifestyle diversification. Using multiple Symbiodinium genomes to detect positive selection, 35 genes were identified, including a gene encoding soluble starch synthase SSY1 and genes related to metabolite secretion, which may be preferred for symbiotic lifestyles. In particular, our in silico analyses revealed that the SSY1 gene family has undergone extensive gene duplications in an ancestral dinoflagellate, and that the mutations detected as positive selection have occurred in the intrinsically disordered region of one of the homologs. Consistent with molecular evolution, the phenotypes of intracellular starch synthesis/accumulation were distinct between the symbiotic and free-living species of Symbiodinium when cultured under different pH and nitrogen conditions. These results provide molecular and phenotypic insights into symbiotic Symbiodinium-coral relationships.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12284398/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144540013","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cell Compartment is a Predictor of Protein Rate of Evolution, but not in the Manner Expected: Evidence Against the Extended Complexity Hypothesis.","authors":"Juan Rivas-Santisteban, Pablo Yubero, Laurence D Hurst","doi":"10.1093/gbe/evaf126","DOIUrl":"10.1093/gbe/evaf126","url":null,"abstract":"<p><p>What accounts for the variation between proteins in their rate of evolution per synonymous substitution (i.e. dN/dS, alias ω)? Previous analyses suggested that cell location is predictive, with intracellular proteins evolving slower than membrane proteins, a result considered supportive of the extended complexity hypothesis. However, as they occur in 3D space, cytoplasmic proteins are expected to be more abundant. As the level of gene expression is the strongest predictor of ω, and many predictors of protein rate variation are explained by covariance with it, here we ask whether the cell compartment effect is explained by covariates. We employ two single-celled species for which there exist exceptional data, the bacterium (Escherichia coli) and the eukaryote (Saccharomyces cerevisiae). For both, we establish informative species trios to determine branch-specific ω values. In both species, in the absence of covariate control, cytoplasmic proteins evolve relatively slowly, while membrane proteins evolve fast, as originally claimed. After controlling for protein abundance, however, membrane proteins have the lowest rates, this inversion being resilient to multiple alternative abundance control methods. The effect size of the cell compartment as a predictor is of a comparable magnitude to the essentiality effect and remains when allowing for essentiality. We conclude that the effects of the cell compartments are real, but their direction is dependent on the presence or absence of abundance control. These results question any model, such as the extended complexity hypothesis, that claims support from a slower evolution of cytoplasmic proteins and underscore the importance of covariate control.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12271741/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144527658","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}