Molecular biology and evolution最新文献_第3页

Fungal-derived tRNAs are expressed and aminoacylated in orchid mitochondria.

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-01-30 DOI: 10.1093/molbev/msaf025

Jessica M Warren, Luis F Ceriotti, M Virginia Sanchez-Puerta, Daniel B Sloan

引用次数: 0

Comparative population genomics unveils congruent secondary suture zone in Southwest Pacific Hydrothermal Vents.

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-01-30 DOI: 10.1093/molbev/msaf024

Tran Lu Y Adrien, Stéphanie Ruault, Claire Daguin-Thiébaut, Anne-Sophie Le Port, Marion Ballenghien, Jade Castel, Pierre-Alexandre Gagnaire, Nicolas Bierne, Sophie Arnaud-Haond, Camille Poitrimol, Eric Thiébaut, François H Lallier, Thomas Broquet, Didier Jollivet, François Bonhomme, Stéphane Hourdez

{"title":"Comparative population genomics unveils congruent secondary suture zone in Southwest Pacific Hydrothermal Vents.","authors":"Tran Lu Y Adrien, Stéphanie Ruault, Claire Daguin-Thiébaut, Anne-Sophie Le Port, Marion Ballenghien, Jade Castel, Pierre-Alexandre Gagnaire, Nicolas Bierne, Sophie Arnaud-Haond, Camille Poitrimol, Eric Thiébaut, François H Lallier, Thomas Broquet, Didier Jollivet, François Bonhomme, Stéphane Hourdez","doi":"10.1093/molbev/msaf024","DOIUrl":"https://doi.org/10.1093/molbev/msaf024","url":null,"abstract":"How the interplay of biotic and abiotic factors shapes current genetic diversity at the community level remains an open question, particularly in the deep sea. Comparative phylogeography of multiple species can reveal the influence of past climatic events, geographic barriers, and species life history traits on spatial patterns of genetic structure across lineages. To shed light on the factors that shape community-level genetic variation and to improve our understanding of deep-sea biogeographic patterns, we conducted a comparative population genomics study on seven hydrothermal vent species co-distributed in the Back-Arc Basins (BABs) of the Southwest Pacific region. Using ddRAD-seq, we compared the range-wide distribution of genomic diversity across species and discovered a shared phylogeographic break. Demogenetic inference revealed shared histories of lineage divergence and a secondary contact. Low levels of asymmetric gene flow probably occurred in most species between the Woodlark and North Fiji basins, but the exact location of contact zones varied from species to species. For two species, we found individuals from the two lineages co-occurring in sympatry in Woodlark Basin. Although species exhibit congruent patterns of spatial structure (Eastern vs Western sites), they also show variation in the degree of divergence among lineages across the suture zone. Our results also show heterogeneous gene flow across the genome, indicating possible partial reproductive isolation between lineages and early speciation. Our comparative study highlights the pivotal role of historical and contemporary factors, underscoring the need for a comprehensive approach-especially in addressing knowledge gaps on the life history traits of deep-sea species.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143066410","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Molecular and functional convergences associated with complex multicellularity in Eukarya.

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-01-29 DOI: 10.1093/molbev/msaf013

Francisco Pereira Lobo, Dalbert Benjamim da Costa, 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 Benjamim da Costa, Thieres Tayroni Martins da Silva, Maycon Douglas de Oliveira","doi":"10.1093/molbev/msaf013","DOIUrl":"https://doi.org/10.1093/molbev/msaf013","url":null,"abstract":"A key trait of Eukarya is the independent evolution of complex multicellular (CM) in animals, 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 (NCT) is commonly used as a quantitative proxy for biological complexity in comparative genomics studies. While expansions of individual gene families have been associated with NCT variation within individual CM lineages, the molecular and functional roles responsible for the independent evolution of CM across Eukarya remain poorly understood. We employed a phylogeny-aware strategy to conduct a genomic-scale search for associations between NCT and the abundance of genomic components across a phylogenetically diverse set of 81 eukaryotic species, including species from all CM lineages. Our annotation schemas represent two complimentary aspects of genomic information: homology - represented by conserved sequences - and function - represented by Gene Ontology (GO) terms. We found many gene families sharing common biological themes that define CM to be independently expanded in two or more CM 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 mechanisms for 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 CM lineages likely due to the common selective pressures in their lifestyles.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A Message from the Editors-in-Chief.

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-01-29 DOI: 10.1093/molbev/msaf022

Brandon Gaut, Claudia Russo

引用次数: 0

Inference of the demographic histories and selective effects of human gut commensal microbiota over the course of human history. 人类历史进程中人类肠道共生菌群的人口历史和选择效应的推断。

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-01-22 DOI: 10.1093/molbev/msaf010

Jonathan C Mah, Kirk E Lohmueller, Nandita Garud

引用次数: 0

Single-cell and spatial transcriptomics illuminate bat immunity and barrier tissue evolution. 单细胞和空间转录组学阐明蝙蝠免疫和屏障组织进化。

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-01-21 DOI: 10.1093/molbev/msaf017

Roy Levinger, Dafna Tussia-Cohen, Sivan Friedman, Yan Lender, Yomiran Nissan, Evgeny Fraimovitch, Yuval Gavriel, Jacqueline Tearle, Aleksandra A Kolodziejczyk, Kyung-Mee Moon, Tomás Gomes, Natalia Kunowska, Maya Weinberg, Giacomo Donati, Leonard J Foster, Kylie R James, Yossi Yovel, Tzachi Hagai

{"title":"Single-cell and spatial transcriptomics illuminate bat immunity and barrier tissue evolution.","authors":"Roy Levinger, Dafna Tussia-Cohen, Sivan Friedman, Yan Lender, Yomiran Nissan, Evgeny Fraimovitch, Yuval Gavriel, Jacqueline Tearle, Aleksandra A Kolodziejczyk, Kyung-Mee Moon, Tomás Gomes, Natalia Kunowska, Maya Weinberg, Giacomo Donati, Leonard J Foster, Kylie R James, Yossi Yovel, Tzachi Hagai","doi":"10.1093/molbev/msaf017","DOIUrl":"https://doi.org/10.1093/molbev/msaf017","url":null,"abstract":"Bats have adapted to pathogens through diverse mechanisms, including increased resistance - rapid pathogen elimination, and tolerance - limiting tissue damage following infection. In the Egyptian fruit bat (an important model in comparative immunology) several mechanisms conferring disease tolerance were discovered, but mechanisms underpinning resistance remain poorly understood. Previous studies on other species suggested that elevated basal expression of innate immune genes may lead to increased resistance to infection. Here, we test whether such transcriptional patterns occur in Egyptian fruit bat tissues through single-cell and spatial transcriptomics of gut, lung and blood cells, comparing gene expression between bat, mouse and human. Despite numerous recent loss and expansion events of interferons in the bat genome, interferon expression and induction are remarkably similar to that of mouse. In contrast, central complement system genes are highly and uniquely expressed in key regions in bat lung and gut epithelium, unlike in human and mouse. Interestingly, the unique expression of these genes in the bat gut is strongest in the crypt, where developmental expression programs are highly conserved. The complement system genes also evolve rapidly in their coding sequence across the bat lineage. Finally, the bat complement system displays strong hemolytic activity. Together, these results indicate a distinctive transcriptional divergence of the complement system, which may be linked to bat resistance, and highlight the intricate evolutionary landscape of bat immunity.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143008510","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Rapid radiation of a plant lineage sheds light on the assembly of dry valley biomes. 植物谱系的快速辐射揭示了干谷生物群落的组装。

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-01-17 DOI: 10.1093/molbev/msaf011

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":"https://doi.org/10.1093/molbev/msaf011","url":null,"abstract":"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.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Read Length Dominates Phylogenetic Placement Accuracy of Ancient DNA Reads. 读取长度支配古代DNA读取的系统发育定位精度。

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-01-17 DOI: 10.1093/molbev/msaf006

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":"https://doi.org/10.1093/molbev/msaf006","url":null,"abstract":"A common problem when analyzing ancient DNA (aDNA) data is to identify the species which corresponds to the recovered aDNA sequence(s). The standard approach is to deploy sequence similarity based tools, such as BLAST. However, as aDNA 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 has deployed only on data from extant sources. Therefore, it is unclear how the aDNA damage affects phylogenetic placement's applicability to aDNA data. To investigate how aDNA damage affects placement accuracy, we re-implemented a statistical model of aDNA damage. We deploy this model, along with a modified version of the existing assessment pipeline PEWO, to seven empirical datasets with four leading tools: APPLES, EPA-NG, pplacer, and RAPPAS. We explore the aDNA damage parameter space via a grid search in order to identify the aDNA 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 aDNA read placement accuracy, and that other factors, such as misincorporations, have a negligible effect on overall placement accuracy.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Navigating a Fine Balance: Point-Mutant Cheater Viruses Disrupt the Viral Replication Cycle. 微妙的平衡：点突变作弊病毒扰乱病毒复制周期。

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-01-06 DOI: 10.1093/molbev/msae258

Moran Meir, Arielle Kahn, Carmel Farage, Yael Maoz, Noam Harel, Adi Ben Zvi, Shir Segev, Maria Volkov, Ravit Yahud, Uri Gophna, Adi Stern

{"title":"Navigating a Fine Balance: Point-Mutant Cheater Viruses Disrupt the Viral Replication Cycle.","authors":"Moran Meir, Arielle Kahn, Carmel Farage, Yael Maoz, Noam Harel, Adi Ben Zvi, Shir Segev, Maria Volkov, Ravit Yahud, Uri Gophna, Adi Stern","doi":"10.1093/molbev/msae258","DOIUrl":"10.1093/molbev/msae258","url":null,"abstract":"Cheater viruses cannot replicate on their own yet replicate faster than the wild type (WT) when the 2 viruses coinfect the same cell. Cheaters must possess dual genetic features: a defect, which leads to their inability to infect cells on their own, and a selective advantage over WT during coinfection. Previously, we have discovered 2 point-mutant cheaters of the MS2 bacteriophage. Here, we set out to discover the possible repertoire of cheater MS2 viruses by performing experimental evolution at a very high multiplicity of infection. Our results revealed a third point-mutant cheater that arose in 8 biological replicas. Each of the 3 primary cheaters disrupts the fine balance necessary for phage replication, in different ways that create a defect + advantage. We found that over time, the point-mutant cheaters accumulate additional secondary mutations, which alter other stages of the viral replication cycle, complementing the disruptions created by the original cheater. Intriguingly, cheater and secondary mutations almost always reside in very close proximity on the genome. This region encodes for multiple functions: overlapping reading frames as well as overlapping RNA structures critical for transitioning from one stage to another in the viral replication cycle. This region of overlap explains the dual functions of cheaters, as one mutation can have pleiotropic effects. Overall, these findings underscore how viruses, whose dense genomes often have overlapping functions, can easily evolve point-mutant cheaters, and how cheaters can evolve to alter the intricate balance of the viral replication cycle.","PeriodicalId":18730,"journal":{"name":"Molecular biology and evolution","volume":" ","pages":""},"PeriodicalIF":11.0,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142864802","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Selection Can Favor a Recombination Landscape That Limits Polygenic Adaptation. 自然选择倾向于限制多基因适应的重组景观。

IF 11 1区生物学

Molecular biology and evolution Pub Date : 2025-01-06 DOI: 10.1093/molbev/msae273

Tom Parée, Luke Noble, Denis Roze, Henrique Teotónio

引用次数: 0