Juan Pablo Marczuk-Rojas, Ana D Maldonado, Lorenzo Carretero-Paulet
{"title":"Episodic and ongoing mechanisms drive plastid-derived nuclear DNA evolution in angiosperms.","authors":"Juan Pablo Marczuk-Rojas, Ana D Maldonado, Lorenzo Carretero-Paulet","doi":"10.1093/gbe/evaf194","DOIUrl":"https://doi.org/10.1093/gbe/evaf194","url":null,"abstract":"<p><p>NUPTs are DNA sequences of plastid origin present in plant nuclear genomes to varying, though typically low, amounts. It is assumed that they are continuously formed and, due to their potentially mutagenic effect, removed at a constant turnover rate, which should result in an exponential decay of their age distributions and a negative correlation between age and size. However, these assumptions are based on analysis from a limited number of species and have never been explicitly tested. To gain insight into the mechanisms driving the origin and evolution of NUPTs, here we surveyed the plastid and nuclear genomes of 30 species representing the main angiosperm (flowering plants) lineages. By modeling the distribution of ages and sizes, examining their linear arrangement across the plastid genome, and statistically assessing spatial biases with respect to other genomic features, we showed that NUPTs are i) formed by both continuous and episodic mechanisms; ii) unevenly represented across the plastid genome; iii) consistently associated with certain classes of RNA genes, in particular rRNA, tRNA and regulatory RNA genes; iv) differentially contributing to structural genes; and v) closer than expected to different superfamilies of transposons in a species-specific manner. Our results reveal the unexpected complexity in the mechanisms driving the origin of NUPTs, which do not only involve their continuous formation but also episodic, highlight their role as a major source of non-coding RNA genes and other genomic features and provide a more complete picture of the different drivers of evolutionary change at the genome level.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145279956","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}
Shahan Derkarabetian, Arianna Lord, Katherine Angier, Julia G Cosgrove, Ella Frigyik, Sara González-Delgado, Breanna Jordan, Paula C Rodríguez-Flores, Shoyo Sato, Lily Shapiro, Gonzalo Giribet
{"title":"Covering all bases: a universal Metazoan UCE probe set to democratize phylogenomics.","authors":"Shahan Derkarabetian, Arianna Lord, Katherine Angier, Julia G Cosgrove, Ella Frigyik, Sara González-Delgado, Breanna Jordan, Paula C Rodríguez-Flores, Shoyo Sato, Lily Shapiro, Gonzalo Giribet","doi":"10.1093/gbe/evaf193","DOIUrl":"https://doi.org/10.1093/gbe/evaf193","url":null,"abstract":"<p><p>Biology is in a genomics era, but many researchers may still be alienated from these techniques as a lack of genomic resources remain for many animal groups, necessitating further democratization. Hybrid capture is a popular phylogenomic approach in molecular systematics, with ultraconserved elements (UCEs) being the most popular. However, access to UCE data is more expensive per sample relative to other commonly used genetic/genomic approaches. Using published genomes, we developed a Metazoan UCE probe set, the universality of which allows multiple research groups working on vastly different animal lineages to share costs and resources across labs. We demonstrated the utility of this probe set both in silico against 58 published metazoan genomes and in vitro with 130 samples representing 33 metazoan phyla, showing that these probes target loci useful for both deep and shallow level relationships. The proportion of target UCEs sequenced by the Metazoa probe is equivalent to that of taxon-specific probe sets, but from across all animal phyla. We explored general patterns of UCE recovery across Metazoa using published genomes and the majority of publicly available UCE probe sets. The Metazoa probe set is commercially available in two forms: the full set, containing 19,986 probes targeting 2146 loci; and the reduced cost set, containing 5098 probes targeting 466 loci. The development of a universal UCE probe set should expand the use of genomic data to a much larger segment of the zoological community, with strong potential for broad applications in phylogenomics across all animal phyla.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145279958","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}
Moisès Bernabeu, Saioa Manzano-Morales, Toni Gabaldón
{"title":"Phylogeny-aware simulations suggest a low impact of unsampled lineages in the inference of gene flow during eukaryogenesis.","authors":"Moisès Bernabeu, Saioa Manzano-Morales, Toni Gabaldón","doi":"10.1093/gbe/evaf190","DOIUrl":"https://doi.org/10.1093/gbe/evaf190","url":null,"abstract":"<p><p>The topologies of gene trees are broadly used to infer horizontal gene transfer events and characterize the potential donor and acceptor partners. Additionally, ratios between branch lengths in the gene tree can inform about the timing of transfers relative to each other. Using this approach, recent studies have proposed a relative chronology of gene acquisitions in the lineage leading to the last eukaryotic common ancestor (LECA). However, a recognised caveat of the branch-length ratio method are potential biases due to incomplete taxon sampling resulting in so-called \"ghost\" lineages. Here, we assessed the effect of ghost lineages on the inference of the relative ordering of gene acquisition events during eukaryogenesis. For this, we used a novel simulation framework that populates a dated Tree of Life with plausible \"ghost\" lineages and simulates their gene transfers to the lineage leading to LECA. Our simulations suggest that a substantial majority of gene acquisitions from distinct ghost donors are inferred with the correct relative order. However, we identify phylogenetic placements where ghost lineages would be more likely to produce misleading results. Overall, our approach offers valuable guidance for the interpretation of future work on eukaryogenesis, and can be readily adapted to other evolutionary scenarios.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145250846","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}
Kristen A Behrens, Zexuan Zhao, Michael R Kidd, Alfred Maluwa, Avner Cnaani, Stephan Koblmüller, Thomas D Kocher
{"title":"Before the East African radiation: sex chromosome systems in basal haplotilapiine cichlids.","authors":"Kristen A Behrens, Zexuan Zhao, Michael R Kidd, Alfred Maluwa, Avner Cnaani, Stephan Koblmüller, Thomas D Kocher","doi":"10.1093/gbe/evaf191","DOIUrl":"https://doi.org/10.1093/gbe/evaf191","url":null,"abstract":"<p><p>Cichlid fishes have undergone an extraordinary diversification in East Africa. They also have a high rate of sex chromosome turnover. This clade provides an opportunity to study the rates and patterns of sex chromosome turnover, and the interactions of sex chromosome turnover with adaptation and speciation. Here we investigate the evolution sex chromosomes in the tribes Tilapiini, Coptodonini, Heterotilapiini, Gobiocichlini, Pelmatolapiini and Oreochromini. We assembled chromosome-scale genomes of male and female Pelmatotilapia mariae. We then mapped pooled sequencing reads for males and females of P. mariae and 12 additional species on several genome assemblies to identify sex chromosomes. Tilapia sparrmanii and Oreochromis aureus share a ZW system on LG3 that overlaps the ZW system identified in P. mariae. Heterotilapia buettikoferi, T. brevimanus and Coptodon bakossiorum share an XY system mapping to another region of LG3. Coptodon zilli, Sarotherodon galilaeus, S. melanotheron and O. niloticus share an XY system on LG1. Finally, O. mossambicus and O. shiranus share an XY system on LG14 and we find evidence of an XY system on LG20 in Danakilia sp. 'shukoray'. The phylogenetic distribution of these sex determination systems suggests a long period of polymorphism for the systems on LG1 and LG3 and a generally lower rate of sex chromosome turnover in these lineages compared to the lacustrine lineages of the East African radiation. Our data is not consistent with the recent suggestion of figla and banf2 as candidate genes for the LG1XY and LG3ZW systems. We suggest a possible role for ubiquitination in the XY systems on LG3.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145250890","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}
Naoko T Fujito, Sundaramoorthy Revathidevi, Yoko Satta, Ituro Inoue
{"title":"Joint effects of balancing selection and population bottlenecks on the evolution of a regulatory region of human anti-viral APOBEC3.","authors":"Naoko T Fujito, Sundaramoorthy Revathidevi, Yoko Satta, Ituro Inoue","doi":"10.1093/gbe/evaf186","DOIUrl":"https://doi.org/10.1093/gbe/evaf186","url":null,"abstract":"<p><p>Human anti-viral APOBEC3s are crucial components of the innate immune response, playing a key role in inhibiting viral replication and proliferation by inducing mutations in viral genomes. In this study, in a regulatory region of ∼16 kb in the APOBEC3 gene cluster on human chromosome 22, we identified three distinct haplogroups that are maintained at high frequencies in both African and non-African populations. Despite the long persistence of these haplogroups, one of which is shared by archaic hominins, the nucleotide diversity within each haplogroup was surprisingly low in non-Africans. Genome-wide empirical distribution and coalescence-based simulation tests showed that the simultaneous observations of low within-haplogroup diversity and high between-haplogroup divergence were incompatible with neutrality. We also identified an ancestral sequence group exclusively in African populations. To explain these features and elucidate the underlying evolutionary mechanisms, we performed forward simulations to model the joint effects of balancing selection and population bottlenecks. The results demonstrated the operation of balancing selection over the past ∼1 million years, as well as a hitherto unexplored reduction in within-haplogroup diversity. The only unexplained observation was the low diversity within African haplogroup I, which is unaffected by the non-African-specific bottleneck. We hypothesized that an extra haplotype turnover within haplogroup I occurred prior to the Out-of-Africa dispersal of modern humans. This study highlights the functional importance of the APOBEC3 regulatory region in terms of evolutionary conservation in Hominidae, a target of natural selection in modern humans, and its relevance in GTEx eQTL.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145232440","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}
T Brock Wooldridge, Merly Escalona, Blair W Perry, Alexis N Enstrom, Dalya Salih, William E Seligmann, Samuel Sacco, Katherine L Moon, Ruta Sahasrabudhe, Noravit Chumchim, Oanh Nguyen, Joanna L Kelley, Ross D E MacPhee, Beth Shapiro
{"title":"Chromosome-scale genomes show rapid diversification and ancient gene flow among bear species.","authors":"T Brock Wooldridge, Merly Escalona, Blair W Perry, Alexis N Enstrom, Dalya Salih, William E Seligmann, Samuel Sacco, Katherine L Moon, Ruta Sahasrabudhe, Noravit Chumchim, Oanh Nguyen, Joanna L Kelley, Ross D E MacPhee, Beth Shapiro","doi":"10.1093/gbe/evaf188","DOIUrl":"https://doi.org/10.1093/gbe/evaf188","url":null,"abstract":"<p><p>Reconstructions of evolutionary history can be restricted by a lack of high quality reference genomes. To-date, only four of the eight species of bears (family Ursidae) have chromosome-level genome assemblies. Here, we present assemblies for three additional species - the sun, sloth, and spectacled bears - and use a whole-genome alignment of all bear species and other carnivores to reconstruct the evolution of Ursidae. Divergence dating based on patterns of coalescence indicates a more rapid diversification than previously reported, with a ∼19 Ma origin for all bears but a ∼3.3 Ma origin for the six species of the subfamily Ursinae. Surprisingly, we observe that nearly 50% of gene tree topologies conflict with our highly supported species tree, a pattern driven by a significant early hybridization event within Ursinae. We also find that the ancestral karyotype of Ursinae has remained largely conserved with the ancestral karyotype of all bears over roughly fifteen million years. In contrast to this stability, dozens of chromosomal fissions and fusions associated with LINE/L1 retrotransposons dramatically restructured the genomes of the giant panda and spectacled bear. Finally, we leverage these genomes to identify species-specific evidence for positive selection on genes associated with color, diet, and metabolism. One of these genes, TCPN2, has a role in pigmentation and shows a series of amino acid mutations in the polar bear over the last 0.5 Ma. Collectively, these new genomic resources enable improved reconstruction of the complex evolutionary history of bears and clarify how this enigmatic group diversified.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145232508","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}
Joris Mordier, Marine Fraisse, Michel Cohen-Tannoudji, Antoine Molaro
{"title":"Recurrent Evolutionary Innovations in Rodent and Primate Schlafen Genes.","authors":"Joris Mordier, Marine Fraisse, Michel Cohen-Tannoudji, Antoine Molaro","doi":"10.1093/gbe/evaf172","DOIUrl":"10.1093/gbe/evaf172","url":null,"abstract":"<p><p>SCHLAFEN proteins are a large family of RNase-related enzymes carrying essential immune and developmental functions. Despite these important roles, Schlafen genes display varying degrees of evolutionary conservation in mammals. While this appears to influence their molecular activities, a detailed understanding of these evolutionary innovations is still lacking. Here, we used in-depth phylogenomic approaches to characterize the evolutionary trajectories and selective forces shaping mammalian Schlafen genes. We traced lineage-specific Schlafen amplifications and found that recent duplicates evolved under distinct selective forces, supporting repeated subfunctionalization cycles. Codon-level natural selection analyses in primates and rodents identified recurrent positive selection over Schlafen protein domains engaged in viral interactions. Combining known crystal structures and predicted protein structures, we discovered a novel class of rapidly evolving residues enriched at the contact interface of SCHLAFEN protein dimers. Our results suggest that inter-SCHLAFEN compatibilities are under strong selective pressures and are likely to impact their molecular functions. We posit that cycles of genetic conflicts with pathogens and between paralogs drove Schlafens' recurrent evolutionary innovations in mammals.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12492265/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145091368","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":"Integrative Genotyping and Analysis of Canine Structural Variation Using Long-read and Short-read Data.","authors":"Peter Z Schall, Jeffrey M Kidd","doi":"10.1093/gbe/evaf173","DOIUrl":"10.1093/gbe/evaf173","url":null,"abstract":"<p><p>Structural variation makes an important contribution to canine evolution and phenotypic differences. Although recent advances in long-read sequencing have enabled the generation of multiple canine genome assemblies, most prior analyses of structural variation have relied on short-read sequencing. To offer a more complete assessment of structural variation in canines, we performed an integrative analysis of structural variants present in 12 canine samples with available long-read and short-read sequencing data along with genome assemblies. Use of long-reads permits the discovery of heterozygous variation that is absent in existing haploid assembly representations while offering a marked increase in the ability to identify insertion variants relative to short-read approaches. Examination of the size spectrum of structural variants shows that dimorphic LINE-1 and SINE variants account for over 45% of all deletions and identified 1,410 LINE-1s with intact open reading frames that show presence-absence dimorphism. Using a graph-based approach, we genotype newly discovered structural variants in an existing collection of 1,879 resequenced dogs and wolves, generating a variant catalog containing a 56.5% increase in the number of deletions and 705% increase in the number of insertions previously found in the analyzed samples. Examination of allele frequencies across admixture components present across breed clades identified 283 structural variants evolving with a signature of selection.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12481690/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145091397","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}
Juan D Carvajal-Castro, Genrietta Yagudayeva, Randy Ortiz, Juan C Santos
{"title":"Global Environmental Factors Impact the Evolution of Adult Hemoglobins in Squamata Reptiles (Lizards and Snakes) and Terrestrial Turtles.","authors":"Juan D Carvajal-Castro, Genrietta Yagudayeva, Randy Ortiz, Juan C Santos","doi":"10.1093/gbe/evaf180","DOIUrl":"10.1093/gbe/evaf180","url":null,"abstract":"<p><p>Convergent evolution of oxygen transport mechanisms arises from respiratory proteins adapting to similar environmental pressures. We examined this relationship between adult hemoglobin subunits (Hbs: HBA1, HBAD, HBB1, and HBB2) found in land reptiles (lizards, snakes, and turtles) with their global distribution variables: Altitude, latitude, ambient temperature, and biomass production. We found that biomass was positively associated with the synonymous substitution rate (dS) of HBAD, while it showed the opposite trend for HBB2 in snakes. Additionally, latitude was negatively related to the dS of HBB2 in snakes, but nonsignificant with other Hbs. Altitude was negatively associated with ω = dN/dS of HBA1 and HBAD, whereas temperature showed a similar negative trend with the ω of HBAD across reptiles and in HBB2 of snakes. At amino acid sites, we found most were conserved except for 11 (two near the heme-binding pocket) across Hbs. These fast-changing sites shifted from polar to nonpolar residues, showing a pattern seen in high-altitude mammals. Our results highlight that in reptiles (i) Hbs are diversifying at individual amino acid sites while generally some subunits exhibiting lower ω rates at higher altitudes and hotter temperatures, with the later and higher biomass ecosystems also linked to increases in dS; (ii) HBBs are the most conserved of the Hbs; (iii) latitudinal gradients only show a significant association with the dS of HBB2 in snakes; and (iv) gene conversion events occurred across HBBs in reptiles, which confound their homology assignation, except for snakes that evidenced a single major duplication in their HBBs.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12504858/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145130650","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}
Jamie D Dixson, Abhijay Azad, Pamela A Padilla, Rajeev K Azad
{"title":"Inference of Cytochrome P450 Evolutionary History Using Structural and Physicochemical Metrics.","authors":"Jamie D Dixson, Abhijay Azad, Pamela A Padilla, Rajeev K Azad","doi":"10.1093/gbe/evaf178","DOIUrl":"10.1093/gbe/evaf178","url":null,"abstract":"<p><p>Cytochrome P450s are a superfamily of heme-binding monooxygenases involved with the detoxification of intrinsic and extrinsic toxins. They are near ubiquitous within biological domains and are found in all domains. Members of families within the superfamily are defined based on amino acid identity thresholds, with thresholds as low as 40% in some families. Relationships among Cytochrome P450 families have proven elusive due to sub-Twilight Zone interfamily identities (<30%) that result in poor multiple sequence alignment quality and thus low levels of support for downstream phylogenetic reconstructions. Despite the low identities, Cytochrome P450 structures are remarkably well conserved both within and among families. In such cases, structural phylogenetics has the potential to unveil elusive relationships because the selectively favored physicochemical properties giving rise to the structure and function of the proteins persist despite sequence-level divergence. Recently, in two separate publications, we demonstrated that by utilizing physicochemical vectors, dynamic time warping, and hierarchical clustering (PCDTW), large swaths of protein domain families and betacoronavirus receptor-binding domain clades were congruent with validated functional/structural relationships. These were important findings because anomalous sequence alignment-based maximum likelihood phylogenetic findings, which were not congruent with the known functional relationships, were resolved. That also validated the use of physicochemical vectors in making inferences about structural/functional homology. Additionally, it illuminated that the same methods might be applied to other protein families with relationships that are difficult to resolve from sequence data alone. Herein, we used Molecular Weight and Hydrophobicity Physicochemical Dynamic Time Warping (MWHP PCDTW) along with structural and sequence alignment-based phylogenetic methodologies to analyze all of the Cytochrome P450s found both in the high-fidelity Structural Classificaction of Proteins (SCOP) database and the reviewed sequences with both experimentally resolved and de novo predicted structures in the Protein Data Bank and the AlphaFold (AF) Protein Structure Database, respectively. We compared the resulting phylogenetic topologies and found that in some cases, structure-based methods may be less able to resolve random/convergent similarity than physicochemical and sequence-based methodologies. This finding agrees with previous findings that demonstrate the usefulness of physicochemical properties in resolving both random structural similarity and potentially convergent relationships.</p>","PeriodicalId":12779,"journal":{"name":"Genome Biology and Evolution","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12502919/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145091130","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}