Ya-Ping Chen, Purayidathkandy Sunojkumar, Robert A Spicer, Richard G J Hodel, Douglas E Soltis, Pamela S Soltis, Alan J Paton, Miao Sun, Bryan T Drew, Chun-Lei Xiang
{"title":"Rapid Radiation of a Plant Lineage Sheds Light on the Assembly of Dry Valley Biomes.","authors":"Ya-Ping Chen, Purayidathkandy Sunojkumar, Robert A Spicer, Richard G J Hodel, Douglas E Soltis, Pamela S Soltis, Alan J Paton, Miao Sun, Bryan T Drew, Chun-Lei Xiang","doi":"10.1093/molbev/msaf011","DOIUrl":"10.1093/molbev/msaf011","url":null,"abstract":"<p><p>Southwest China is characterized by high plateaus, large mountain systems, and deeply incised dry valleys formed by major rivers and their tributaries. Despite the considerable attention given to alpine plant radiations in this region, the timing and mode of diversification of the numerous dry valley plant lineages remain unknown. To address this knowledge gap, we investigated the macroevolution of Isodon (Lamiaceae), a lineage commonly distributed in the dry valleys in southwest China and wetter areas of Asia and Africa. We reconstructed a robust phylogeny encompassing nearly 90% of the approximately 140 extant Isodon species using transcriptome and genome-resequencing data. Our results suggest a rapid radiation of Isodon during the Pliocene that coincided with a habit shift from herbs to shrubs and a habitat shift from humid areas to dry valleys. The shrubby growth form likely acted as a preadaptation allowing for the movement of Isodon species into these dry valleys. Ecological analyses highlight drought-related factors as key drivers influencing the niche preferences of different growth forms and species richness of Isodon. The interplay between topography and the development of the East Asian monsoon since the middle Miocene likely contributed to the formation of the dry valley biome in southwest China. This study enhances our understanding of evolutionary dynamics and ecological drivers shaping the distinctive flora of southwest China and reveals the strategies employed by montane plants in response to climate change and dryland expansion, thus facilitating conservation efforts globally.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11817785/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143008440","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}
{"title":"The Convergent Evolution of Hummingbird Pollination Results in Repeated Floral Scent Loss Through Gene Downregulation.","authors":"Kathy Darragh, Kathleen M Kay, Santiago R Ramírez","doi":"10.1093/molbev/msaf027","DOIUrl":"10.1093/molbev/msaf027","url":null,"abstract":"<p><p>The repeated evolution of the same trait in different lineages provides powerful natural experiments to study the phenotypic and genotypic predictability of trait gain and loss. A fascinating example is the repeated evolution of hummingbird pollination in plant lineages in the Americas, a widespread and often unidirectional phenomenon. The spiral gingers in the genus Costus are ancestrally bee pollinated, and hummingbird pollination has evolved multiple times independently in the tropical Americas. These pollinator transitions are accompanied by predictable morphological and color changes, but the changes in floral scent have not been described. In this study, we describe the floral scent composition of 30 species of Costus sampled across the phylogeny to understand how floral scent has evolved across the genus with respect to pollinator transitions. We then combine transcriptomics and genomics to identify gene expression differences and gene family evolution associated with pollinator transitions. We show that hummingbird-pollinated species have mostly lost their floral scent, whereas bee-pollinated species exhibit either floral scent maintenance or, in some cases, gains of more diverse scent profiles. We find the floral scent loss appears to be due to gene downregulation rather than pseudogenization. The remarkable consistency of scent loss in hummingbird-pollinated species highlights the shared strong selection pressures experienced by these lineages. Even species with more recent transitions from bee to hummingbird pollination exhibit scent loss, highlighting the rapid breakdown of scent emission following pollinator transitions. This research highlights the capacity for rapid changes when selection pressures are strong through downregulation of floral scent genes.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11848715/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143080480","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}
Ben Bettisworth, Nikolaos Psonis, Nikos Poulakakis, Pavlos Pavlidis, Alexandros Stamatakis
{"title":"Read Length Dominates Phylogenetic Placement Accuracy of Ancient DNA Reads.","authors":"Ben Bettisworth, Nikolaos Psonis, Nikos Poulakakis, Pavlos Pavlidis, Alexandros Stamatakis","doi":"10.1093/molbev/msaf006","DOIUrl":"10.1093/molbev/msaf006","url":null,"abstract":"<p><p>A common problem when analyzing ancient DNA data is to identify the species that corresponds to the recovered analyzing ancient DNA sequence(s). The standard approach is to deploy sequence similarity-based tools, such as BLAST. However, as analyzing ancient DNA reads may frequently stem from unsampled taxa due to extinction, it is likely that there is no exact match in any database. As a consequence, these tools may not be able to accurately place such reads in a phylogenetic context. Phylogenetic placement is a technique where a read is placed onto a specific branch of a phylogenetic reference tree, which allows for a substantially finer resolution when identifying reads. Prior applications of phylogenetic placement have deployed only on data from extant sources. Therefore, it is unclear how the analyzing ancient DNA damage affects phylogenetic placement's applicability to analyzing ancient DNA data. To investigate how analyzing ancient DNA damage affects placement accuracy, we re-implemented a statistical model of analyzing ancient DNA damage. We deploy this model, along with a modified version of the existing assessment pipeline PEWO, to 7 empirical datasets with 4 leading tools: APPLES, EPA-Ng, pplacer, and RAPPAS. We explore the analyzing ancient DNA damage parameter space via a grid search in order to identify the analyzing ancient DNA damage factors that exhibit the largest impact on placement accuracy. We find that the frequency of DNA backbone nicks (and consequently read length) has the, by far, largest impact on analyzing ancient DNA read placement accuracy, and that other factors, such as misincorporations, have a negligible effect on overall placement accuracy.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11839404/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143008447","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}
Jess D Hebert, Yuning J Tang, Márton Szamecz, Laura Andrejka, Steven S Lopez, Dmitri A Petrov, Gábor Boross, Monte M Winslow
{"title":"Combinatorial In Vivo Genome Editing Identifies Widespread Epistasis and an Accessible Fitness Landscape During Lung Tumorigenesis.","authors":"Jess D Hebert, Yuning J Tang, Márton Szamecz, Laura Andrejka, Steven S Lopez, Dmitri A Petrov, Gábor Boross, Monte M Winslow","doi":"10.1093/molbev/msaf023","DOIUrl":"10.1093/molbev/msaf023","url":null,"abstract":"<p><p>Lung adenocarcinoma, the most common subtype of lung cancer, is genomically complex, with tumors containing tens to hundreds of non-synonymous mutations. However, little is understood about how genes interact with each other to enable the evolution of cancer in vivo, largely due to a lack of methods for investigating genetic interactions in a high-throughput and quantitative manner. Here, we employed a novel platform to generate tumors with inactivation of pairs of ten diverse tumor suppressor genes within an autochthonous mouse model of oncogenic KRAS-driven lung cancer. By quantifying the fitness of tumors with every single and double mutant genotype, we show that most tumor suppressor genetic interactions exhibited negative epistasis, with diminishing returns on tumor fitness. In contrast, Apc inactivation showed positive epistasis with the inactivation of several other genes, including synergistic effects on tumor fitness in combination with Lkb1 or Nf1 inactivation. Sign epistasis was extremely rare, suggesting a surprisingly accessible fitness landscape during lung tumorigenesis. These findings expand our understanding of the interactions that drive tumorigenesis in vivo.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11824425/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143189873","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}
Fanny E Hartmann, Ricardo C Rodríguez de la Vega, Arthur Demené, Thomas Badet, Jean-Philippe Vernadet, Quentin Rougemont, Amandine Labat, Alodie Snirc, Lea Stauber, Daniel Croll, Simone Prospero, Cyril Dutech, Tatiana Giraud
{"title":"An Inversion Polymorphism Under Balancing Selection, Involving Giant Mobile Elements, in an Invasive Fungal Pathogen.","authors":"Fanny E Hartmann, Ricardo C Rodríguez de la Vega, Arthur Demené, Thomas Badet, Jean-Philippe Vernadet, Quentin Rougemont, Amandine Labat, Alodie Snirc, Lea Stauber, Daniel Croll, Simone Prospero, Cyril Dutech, Tatiana Giraud","doi":"10.1093/molbev/msaf026","DOIUrl":"10.1093/molbev/msaf026","url":null,"abstract":"<p><p>Recombination suppression can evolve in sex or mating-type chromosomes, or in autosomal supergenes, with different haplotypes being maintained by balancing selection. In the invasive chestnut blight fungus Cryphonectria parasitica, a genomic region was suggested to lack recombination and to be partially physically linked to the mating-type (MAT) locus based on segregation analyses. Using hundreds of available C. parasitica genomes and generating new high-quality genome assemblies, we show that a ca. 1.2 Mb genomic region proximal to the mating-type locus lacks recombination, with the segregation of two highly differentiated haplotypes in balanced proportions in invasive populations. High-quality genome assemblies further revealed an inversion in one of the haplotypes in the invaded range. The two haplotypes were estimated to have diverged 1.5 million years ago, and each harboured specific genes, some of which likely belonging to Starships. These are large transposable elements, mobilized by tyrosine recombinases, able to move accessory genes, and involved in adaptation in multiple fungi. The MAT-proximal region carried genes upregulated under virus infection or vegetative incompatibility reaction. In the native range, the MAT-proximal region also appeared to have a different evolutionary history than the rest of the genome. In all continents, the MAT-Proximal region was enriched in nonsynonymous substitutions, in gene presence/absence polymorphism, in tyrosine recombinases and in transposable elements. This study thus sheds light on a case of a large nonrecombining region partially linked to a mating compatibility locus, likely maintained by balancing selection on differentiated haplotypes, possibly involved in adaptation in a devastating tree pathogen.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11848846/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143189871","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}
Francisco Pereira Lobo, Dalbert Macedo Benjamim, Thieres Tayroni Martins da Silva, Maycon Douglas de Oliveira
{"title":"Molecular and Functional Convergences Associated with Complex Multicellularity in Eukarya.","authors":"Francisco Pereira Lobo, Dalbert Macedo Benjamim, Thieres Tayroni Martins da Silva, Maycon Douglas de Oliveira","doi":"10.1093/molbev/msaf013","DOIUrl":"10.1093/molbev/msaf013","url":null,"abstract":"<p><p>A key trait of Eukarya is the independent evolution of complex multicellularity in animals, land plants, fungi, brown algae, and red algae. This phenotype is characterized by the initial exaptation of cell-cell adhesion genes followed by the emergence of mechanisms for cell-cell communication, together with the expansion of transcription factor gene families responsible for cell and tissue identity. The number of cell types is commonly used as a quantitative proxy for biological complexity in comparative genomics studies. While expansions of individual gene families have been associated with variations in the number of cell types within individual complex multicellular lineages, the molecular and functional roles responsible for the independent evolution of complex multicellular across Eukarya remain poorly understood. We employed a phylogeny-aware strategy to conduct a genomic-scale search for associations between the number of cell types and the abundance of genomic components across a phylogenetically diverse set of 81 eukaryotic species, including species from all complex multicellular lineages. Our annotation schemas represent 2 complimentary aspects of genomic information: homology, represented by conserved sequences, and function, represented by Gene Ontology terms. We found many gene families sharing common biological themes that define complex multicellular to be independently expanded in 2 or more complex multicellular lineages, such as components of the extracellular matrix, cell-cell communication mechanisms, and developmental pathways. Additionally, we describe many previously unknown associations of biological themes and biological complexity, such as expansions of genes playing roles in wound response, immunity, cell migration, regulatory processes, and response to natural rhythms. Together, our findings unveil a set of functional and molecular convergences independently expanded in complex multicellular lineages likely due to the common selective pressures in their lifestyles.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11827588/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143059224","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}
Xian Shi, Cheng Ma, Ningbo Chen, Ming-Min Xu, Sumaya Kambal, Zheng-Fei Cai, Qiwen Yang, Adeniyi C Adeola, Li-Sheng Liu, Jun Wang, Wen-Fa Lu, Yan Li, George M Msalya, Chuzhao Lei, Joram M Mwacharo, Jian-Lin Han, Olivier Hanotte, Ya-Ping Zhang, Min-Sheng Peng
{"title":"Selection Increases Mitonuclear DNA Discordance but Reconciles Incompatibility in African Cattle.","authors":"Xian Shi, Cheng Ma, Ningbo Chen, Ming-Min Xu, Sumaya Kambal, Zheng-Fei Cai, Qiwen Yang, Adeniyi C Adeola, Li-Sheng Liu, Jun Wang, Wen-Fa Lu, Yan Li, George M Msalya, Chuzhao Lei, Joram M Mwacharo, Jian-Lin Han, Olivier Hanotte, Ya-Ping Zhang, Min-Sheng Peng","doi":"10.1093/molbev/msaf039","DOIUrl":"10.1093/molbev/msaf039","url":null,"abstract":"<p><p>Mitochondrial function relies on the coordinated interactions between genes in the mitochondrial DNA and nuclear genomes. Imperfect interactions following mitonuclear incompatibility may lead to reduced fitness. Mitochondrial DNA introgressions across species and populations are common and well documented. Various strategies may be expected to reconcile mitonuclear incompatibility in hybrids or admixed individuals. African admixed cattle (Bos taurus × B. indicus) show sex-biased admixture, with taurine (B. taurus) mitochondrial DNA and a nuclear genome predominantly of humped zebu (B. indicus). Here, we leveraged local ancestry inference approaches to identify the ancestry and distribution patterns of nuclear functional genes associated with the mitochondrial oxidative phosphorylation process in the genomes of African admixed cattle. We show that most of the nuclear genes involved in mitonuclear interactions are under selection and of humped zebu ancestry. Variations in mitochondrial DNA copy number may have contributed to the recovery of optimal mitochondrial function following admixture with the regulation of gene expression, alleviating or nullifying mitochondrial dysfunction. Interestingly, some nuclear mitochondrial genes with enrichment in taurine ancestry may have originated from ancient African aurochs (B. primigenius africanus) introgression. They may have contributed to the local adaptation of African cattle to pathogen burdens. Our study provides further support and new evidence showing that the successful settlement of cattle across the continent was a complex mechanism involving adaptive introgression, mitochondrial DNA copy number variation, regulation of gene expression, and selection of ancestral mitochondria-related genes.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11879056/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143374247","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}
Kate R Castellano, Michelle L Neitzey, Andrew Starovoitov, Gabriel A Barrett, Noah M Reid, Vidya S Vuruputoor, Cynthia N Webster, Jessica M Storer, Nicole R Pauloski, Natalie J Ameral, Susan L McEvoy, M Conor McManus, Jonathan B Puritz, Jill L Wegrzyn, Rachel J O'Neill
{"title":"Genome Assembly of a Living Fossil, the Atlantic Horseshoe Crab Limulus polyphemus, Reveals Lineage-Specific Whole-Genome Duplications, Transposable Element-Based Centromeres, and a ZW Sex Chromosome System.","authors":"Kate R Castellano, Michelle L Neitzey, Andrew Starovoitov, Gabriel A Barrett, Noah M Reid, Vidya S Vuruputoor, Cynthia N Webster, Jessica M Storer, Nicole R Pauloski, Natalie J Ameral, Susan L McEvoy, M Conor McManus, Jonathan B Puritz, Jill L Wegrzyn, Rachel J O'Neill","doi":"10.1093/molbev/msaf021","DOIUrl":"10.1093/molbev/msaf021","url":null,"abstract":"<p><p>Horseshoe crabs, considered living fossils with a stable morphotype spanning ∼445 million years, are evolutionarily, ecologically, and biomedically important species experiencing rapid population decline. Of the four extant species of horseshoe crabs, the Atlantic horseshoe crab, Limulus polyphemus, has become an essential component of the modern medicine toolkit. Here, we present the first chromosome-level genome assembly, and the most contiguous and complete assembly to date, for L. polyphemus using nanopore long-read sequencing and chromatin conformation analysis. We find support for three horseshoe crab-specific whole-genome duplications, but none shared with Arachnopulmonata (spiders and scorpions). Moreover, we discovered tandem duplicates of endotoxin detection pathway components Factors C and G, identify candidate centromeres consisting of Gypsy retroelements, and classify the ZW sex chromosome system for this species and a sister taxon, Carcinoscorpius rotundicauda. Finally, we revealed this species has been experiencing a steep population decline over the last 5 million years, highlighting the need for international conservation interventions and fisheries-based management for this critical species.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11836539/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143189880","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}
Emma Y Roback, Estephany Ferrufino, Rachel L Moran, Devin Shennard, Charlotte Mulliniks, Josh Gallop, James Weagley, Jeffrey Miller, Yaouen Fily, Claudia Patricia Ornelas-García, Nicolas Rohner, Johanna E Kowalko, Suzanne E McGaugh
{"title":"Population Genomics of Premature Termination Codons in Cavefish With Substantial Trait Loss.","authors":"Emma Y Roback, Estephany Ferrufino, Rachel L Moran, Devin Shennard, Charlotte Mulliniks, Josh Gallop, James Weagley, Jeffrey Miller, Yaouen Fily, Claudia Patricia Ornelas-García, Nicolas Rohner, Johanna E Kowalko, Suzanne E McGaugh","doi":"10.1093/molbev/msaf012","DOIUrl":"10.1093/molbev/msaf012","url":null,"abstract":"<p><p>Loss-of-function alleles are a pertinent source of genetic variation with the potential to contribute to adaptation. Cave-adapted organisms exhibit striking loss of ancestral traits such as eyes and pigment, suggesting that loss-of-function alleles may play an outsized role in these systems. Here, we leverage 141 whole genome sequences to evaluate the evolutionary history and adaptive potential of single nucleotide premature termination codons (PTCs) in Mexican tetra. We find that cave populations contain significantly more PTCs at high frequency than surface populations. We also find that PTCs occur more frequently in genes with inherent relaxed evolutionary constraint relative to the rest of the genome. Using SLiM to simulate PTC evolution in a cavefish population, we show that the smaller population size and increased genetic drift is sufficient to account for the observed increase in PTC frequency in cave populations without positive selection. Using CRISPR-Cas9, we show that mutation of one of these genes, pde6c, produces phenotypes in surface Mexican tetra that mimic cave-derived traits. Finally, we identify a small subset of candidate genes that contain high-frequency PTCs in cave populations, occur within selective sweeps, and may contribute to beneficial traits such as reduced energy expenditure, suggesting that a handful of PTCs may be adaptive. Overall, our work provides a rare characterization of PTCs across wild populations and finds that they may have an important role in loss-of-function phenotypes, contributing to a growing body of literature showing genome evolution through relaxed constraint in subterranean organisms.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11796094/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143008435","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}
Léa Bou Dagher, Dominique Madern, Philippe Malbos, Céline Brochier-Armanet
{"title":"Faithful Interpretation of Protein Structures through Weighted Persistent Homology Improves Evolutionary Distance Estimation.","authors":"Léa Bou Dagher, Dominique Madern, Philippe Malbos, Céline Brochier-Armanet","doi":"10.1093/molbev/msae271","DOIUrl":"10.1093/molbev/msae271","url":null,"abstract":"<p><p>Phylogenetic inference is mainly based on sequence analysis and requires reliable alignments. This can be challenging, especially when sequences are highly divergent. In this context, the use of three-dimensional protein structures is a promising alternative. In a recent study, we introduced an original topological data analysis method based on persistent homology to estimate the evolutionary distances from structures. The method was successfully tested on 518 protein families representing 22,940 predicted structures. However, as anticipated, the reliability of the estimated evolutionary distances was impacted by the quality of the predicted structures and the presence of indels in the proteins. This paper introduces a new topological descriptor, called bio-topological marker (BTM), which provides a more faithful description of the structures, a topological analysis for estimating evolutionary distances from BTMs, and a new weight-filtering method adapted to protein structures. These new developments significantly improve the estimation of evolutionary distances and phylogenies inferred from structures.</p>","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11789942/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143123381","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}