MOLECULAR BIOLOGY AND EVOLUTION 在分子（包括基因组学）和进化生物学的界面发表研究。我们考虑包含人口、分类、功能和表型组织各个层次的模式、过程和预测的手稿。除了具有更广泛范围和影响的基本发现外，我们还对出版新的和改进的方法、资源、技术和理论感兴趣，这些方法、资源、技术和理论将显着推进进化研究。我们还发表了对基因组进化最新发展的平衡评论和前瞻性观点，提出了分子进化领域或应用的未来方向。

The journal "Molecular Biology and Evolution" focuses on the interface of molecular biology and evolutionary biology, publishing research in this area. We welcome manuscripts that address patterns, processes, and predictions across various levels, including population, taxonomy, function, and phenotype. In addition to fundamental findings with broad implications, we are also interested in publishing new and improved methods, resources, technologies, and theories that significantly advance evolutionary research. Furthermore, we publish balanced reviews and forward-looking perspectives on the latest developments in genome evolution, proposing future directions for the field of molecular evolution and its applications.

《Molecular Biology and Evolution》期刊专注于分子生物学与进化生物学的交叉领域，发表相关研究成果。我们欢迎涉及种群、分类、功能和表型等多个层面的模式、过程和预测的手稿。除了具有广泛影响的基础研究发现外，我们也对新的和改进的方法、资源、技术和理论感兴趣，这些内容将显著推动进化研究的发展。此外，我们还发表关于基因组进化最新进展的综合评论和前瞻性观点，探讨分子进化领域及其应用的未来方向。

Molecular Biology and Evolution

Following invasion, insects can become adapted to conditions experienced in their invasive range, but there are few studies on the speed of adaptation and its genomic basis. Here, we examine a small insect pest, Thrips palmi, following its contemporary range expansion across a sharp climate gradient from the subtropics to temperate areas. We first found a geographically associated population genetic structure and inferred a stepping-stone dispersal pattern in this pest from the open fields of southern China to greenhouse environments of northern regions, with limited gene flow after colonization. In common garden experiments, both the field and greenhouse groups exhibited clinal patterns in thermal tolerance as measured by critical thermal maximum (CTmax) closely linked with latitude and temperature variables. A selection experiment reinforced the evolutionary potential of CTmax with an estimated h2 of 6.8% for the trait. We identified 3 inversions in the genome that were closely associated with CTmax, accounting for 49.9%, 19.6%, and 8.6% of the variance in CTmax among populations. Other genomic variations in CTmax outside the inversion region were specific to certain populations but functionally conserved. These findings highlight rapid adaptation to CTmax in both open field and greenhouse populations and reiterate the importance of inversions behaving as large-effect alleles in climate adaptation.

Li-Jun Ma

Li-Jun Cao

Jin-Cui Chen

Meng-Qing Tang

Wei Song

Fang-Yuan Yang

Xiu-Jing Shen

Ya-Jing Ren

Qiong Yang

Hu Li

Ary Anthony Hoffmann

Shu-Jun Wei

Rapid and Repeated Climate Adaptation Involving Chromosome Inversions following Invasion of an Insect

The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.

Sudhir Kumar

Glen Stecher

Michael Li

Christina Knyaz

Koichiro Tamura

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

MEGA X：跨计算平台的分子进化遗传分析

Abstract Even though gene duplication is a key source of new genes and evolutionary innovation, it is unclear how duplicates survive the period immediately following gene duplication, in which both copies are functionally redundant. In the absence of epigenetic silencing, the abundance of the gene product would double after gene duplication, which would often have deleterious effects. However, recent duplicates exhibit low expression levels, which could be at least partially explained by high levels of promoter methylation. What evolutionary paths lead to duplicate hypermethylation, and does it affect both duplicates, or only one? Here, we compare levels of promoter methylation in 10 human and 16 mouse tissues, between singletons and duplicates and among human-mouse orthologs of different kinds (one-to-one, one-to-many, many-to-one, and many-to-many). Our results indicate that: (1) on average, duplicates are more methylated than singletons in mouse, but less methylated than singletons in human, (2) recently duplicated genes tend to exhibit high levels of promoter methylation, (3) genes that undergo duplication tend to be highly methylated before duplication, (4) after gene duplication, one of the copies (the daughter copy, i.e. the one that relocates to a new genomic context) tends to undergo an additional increase in promoter methylation, whereas the other (the parental copy, which remains in the original genomic location) tends to retain pre-duplication methylation levels, and (5) daughter copies tend to be lowly expressed. These observations support a model in which daughter copies are repressed via promoter hypermethylation and can thus survive the filter of purifying selection until both copies diverge functionally.

Mercedes de la Fuente

Isabel Mendizabal

Mira Han

Soojin V Yi

David Alvarez-Ponce

Asymmetrical evolution of promoter methylation of mammalian genes after duplication

哺乳动物基因重复后启动子甲基化的不对称演化

The sequential order of genes in animal mitochondrial DNA tends to be conserved at high taxonomic levels. Consequently, when mitochondrial gene rearrangements occur, they can provide compelling markers of ancient phylogenetic history (see reviews in Boore, Daehler, and Brown [1999], Saccone et al. [1999], and references therein). Such gene order characters have proven particularly useful for resolving deep-branching events characterizing superphyla, phyla, and classes, a scale over which nucleotide sequence analysis has often proven problematic (e.g., Smith et al. 1993; Boore and Brown 1994a, 1998, 2000; Boore et al. 1995; Boore, Lavrov, and Brown 1998; Stechmann and Schlegel 1999). Most frequently, these rearrangements are associated with the movement of tRNA genes which, based on their stem-and-loop structure, may also have an underlying role as mobilizing elements within the mitochondrial genome (Moritz and Brown 1987; Stanton et al. 1994; Saccone et al. 1999). Gene rearrangements involving ribosomal and protein-encoding genes (hereinafter referred to as ‘‘major’’ genes), however, are much rarer. Here we report a mitochondrial gene rearrangement involving major genes that has occurred within a genus of marine vermetid gastropods that diversified within the Cenozoic. Based on data from the fossil record and an independent molecular calibration, we estimate that this gene order change may have occurred within the last 38–48 Myr, making this a very recent major gene order rearrangement. This finding thus has important implications for the use of gene order characters in metazoan phylogeny, in terms of both understanding the mechanism of gene order rearrangements and determining the taxonomic level and timescale over which these major rearrangements may prove useful. The family Vermetidae comprises seven genera with ;100 extant species of sessile, uncoiled, suspension-feeding gastropods found in shallow marine waters in warm temperate to tropical latitudes throughout the world (Keen 1961; Morton 1965; unpublished data). Based on our current understanding of gastropod evolution, vermetid gastropods radiated from a basal caenogastropod stock sometime in the early Cenozoic (Keen 1961; unpublished data). As part of a study to investi-

Timothy A. Rawlings

Timothy M. Collins

Rüdiger Bieler

A Major Mitochondrial Gene Rearrangement Among Closely Related Species

密切相关物种间的主要线粒体基因重排

Avian genomes are small and lack some genes that are conserved in the genomes of most other vertebrates including nonavian sauropsids. One hypothesis stated that paralogs may provide biochemical or physiological compensation for certain gene losses; however, no functional evidence has been reported to date. By integrating evolutionary analysis, physiological genomics, and experimental gene interference, we clearly demonstrate functional compensation for gene loss. A large-scale phylogenetic analysis of over 1,400 SLC2 gene sequences identifies six new SLC2 genes from nonmammalian vertebrates and divides the SLC2 gene family into four classes. Vertebrates retain class III SLC2 genes but partially lack the more recent duplicates of classes I and II. Birds appear to have completely lost the SLC2A4 gene that encodes an important insulin-sensitive GLUT in mammals. We found strong evidence for positive selection, indicating that the N-termini of SLC2A4 and SLC2A12 have undergone diversifying selection in birds and mammals, and there is a significant correlation between SLC2A12 functionality and basal metabolic rates in endotherms. Physiological genomics have uncovered that SLC2A12 expression and allelic variants are associated with insulin sensitivity and blood glucose levels in wild birds. Functional tests have indicated that SLC2A12 abrogation causes hyperglycemia, insulin resistance, and high relative activity, thus increasing energy expenditures that resemble a diabetic phenotype. These analyses suggest that the SLC2A12 gene not only functionally compensates insulin response for SLC2A4 loss but also affects daily physical behavior and basal metabolic rate during bird evolution, highlighting that older genes retain a higher level of functional diversification.

Ying Xiong

Fumin Lei

SLC2A12of SLC2 Gene Family in Bird Provides Functional Compensation for the Loss ofSLC2A4Gene in Other Vertebrates

Abstract Cheater viruses cannot replicate on their own yet replicate faster than the wild type (WT) when the two 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 co-infection. Previously, we have discovered two 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 (MOI). Our results revealed a third point-mutant cheater that arose in eight biological replicas. Each of the three 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.

Moran Meir

Arielle Kahn

Carmel Farage

Yael Maoz

Noam Harel

Adi Ben Zvi

Shir Segev

Maria Volkov

Ravit Yahud

Uri Gophna

Adi Stern

Navigating a fine balance: point-mutant cheater viruses disrupt the viral replication cycle

巧妙平衡的导航：点突变欺骗性病毒破坏病毒复制周期

Abstract Microbial communities that maintain symbiotic relationships with animals evolve by adapting to the specific environmental niche provided by their host, yet understanding their patterns of speciation remains challenging. Whether bacterial speciation occurs primarily through allopatric or sympatric processes remains an open question. In addition, patterns of DNA transfers, which are pervasive in bacteria, are more constrained in a closed host-gut system. Eusocial bees have co-evolved with their specialized microbiota for over 85 million years, constituting a simple and valuable system to study the complex dynamics of host-associated microbial interactions. Here we studied the patterns of speciation and evolution of seven specialized gut bacteria from three clades of eusocial bee species: western honey bees, eastern honey bees and bumblebees. We conducted genomic analyses to infer species delineation relative to the patterns of homologous recombination (HR), and horizontal gene transfer (HGT). The studied bacteria presented various modes of evolution and speciation relative to their hosts, but some trends were consistent across all of them. We observed a clear interruption of homologous recombination between bacteria inhabiting different bee hosts, which is consistent with a mechanism of allopatric speciation, but we also identified interruptions of homologous recombination within hosts, suggesting recent or ongoing sympatric speciation. In contrast to HR, we observed that HGT events were not constrained by species borders. Overall, our findings show that in host-associated bacterial populations, patterns of HR and HGT have different impacts on speciation patterns, which are driven by both allopatric and sympatric speciation processes.

Caroline Stott

Awa Diop

Kasie Raymann

Louis-Marie Bobay

Co-evolution and Gene Transfers Drive Speciation Patterns in Host-Associated Bacteria

宿主相关细菌的物种形成模式由协同进化和基因转移驱动

The impact of gene loss on the diversification of taxa and the emergence of evolutionary innovations remains poorly understood. Here, our investigation on the evolution of the Fibroblast Growth Factors (FGFs) in appendicularian tunicates as a case study reveals a scenario of "less, but more" characterized by massive losses of all Fgf gene subfamilies, except for the Fgf9/16/20 and Fgf11/12/13/14, which in turn underwent two bursts of duplications. Through phylogenetic analysis, synteny conservation, and gene and protein structure, we reconstruct the history of appendicularian Fgf genes, highlighting their paracrine and intracellular functions. Exhaustive analysis of developmental Fgf expression in Oikopleura dioica allow us to identify four associated evolutionary patterns characterizing the "less, but more" conceptual framework: conservation of ancestral functions; function shuffling between paralogs linked to gene losses; innovation of new functions after the duplication bursts; and function extinctions linked to gene losses. Our findings allow us to formulate novel hypotheses about the impact of Fgf losses and duplications on the transition from an ancestral ascidian-like biphasic lifestyle to the fully free-living appendicularians. These hypotheses include massive co-options of Fgfs for the development of the oikoblast and the tail fin; recruitment of Fgf11/12/13/14s into the evolution of a new mouth, and their role modulating neuronal excitability; the evolutionary innovation of an anterior tail FGF signaling source upon the loss of retinoic acid signaling; and the potential link between the loss of Fgf7/10/22 and Fgf8/17/18 and the loss of drastic metamorphosis and tail absorption in appendicularians, in contrast to ascidians.

Gaspar Sánchez-Serna

Jordi Badia-Ramentol

Paula Bujosa

Alfonso Ferrández-Roldán

Nuria P Torres-Águila

Marc Fabregà-Torrus

Johannes N Wibisana

Michael J Mansfield

Charles Plessy

Nicholas M Luscombe

Ricard Albalat

Cristian Cañestro

Less, but more: new insights from appendicularians on chordate Fgf evolution and the divergence of tunicate lifestyles

少而精：尾海鞘纲对脊索动物Fgf进化及被囊动物生活方式分化的全新见解

Abstract Marine mammals have evolved unihemispheric slow wave sleep (USWS), a unique state during which one cerebral hemisphere sleeps while the other remains awake, to mitigate the fundamental conflict between sleep and wakefulness. However, the underlying mechanisms remain largely unclear. Here, we use a comparative phylogenetic approach to analyze genes associated with light-dependent circadian mechanisms, aiming to reconstruct the evolution of the circadian rhythm pathway in mammals and to identify adaptively changed components likely to have contributed to the development of USWS. Specifically, among eight genes with shared signals of positive selection in two USWS-specific lineages, seven genes showed direct evidence of affecting sleep and spontaneous movements. Both in vitro and in vivo experiments indicated that functional innovation in cetacean and non-phocid pinniped FBXL21, which was found to undergo positive selection, may be beneficial for decoupling sleep–wake patterns from daily rhythms to sustain continuous swimming. For cetaceans exhibiting only USWS, we identified 73 genes as rapidly evolving and 92 genes containing unique amino acid substitutions. Functional assays showed that a cetacean-specific mutation (F411Y) in NFIL3 led to a decrease in repressor activity and protein stability. Furthermore, convergent amino acid replacements detected in genes related to Ca2+ signaling and CREB phosphorylation suggest their crucial role in USWS adaptation. Overall, this study enhances our understanding of the evolutionary mechanisms underlying USWS and provides a foundation for investigating how circadian rhythm changes contribute to variations in sleep and circadian behavior.

Daiqing Yin

Zhenpeng Yu

Haojia Jiang

Yujie Chong

Cuijuan Zhong

Shixia Xu

Guang Yang

Circadian rhythm mechanisms underlying convergent adaptation of unihemispheric slow-wave sleep in marine mammals

海洋哺乳动物单侧半球慢波睡眠趋同适应的昼夜节律机制

Abbreviation	Mol Biol Evol
Journal Impact	11.08
Quartiles(Global)	GENETICS & HEREDITY(Q1)

ISSN	0737-4038, 1537-1719
h-index	245
Top Journals	Yes

Publication Information	Publisher: Oxford University Press，Publishing cycle: Monthly，Journal Type: journal，Open Access Journals: Yes
Basic data	Year of publication: 1983，Proportion of original research papers: 99.25%，Self Citation Rate:2.70%， Gold OA Rate: 95.42%
Journal Fees	$3255Details
Average review cycle	网友分享经验：平均1.0个月
Average recruitment ratio	网友分享经验：很难

Molecular Biology and Evolution

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Rapid and Repeated Climate Adaptation Involving Chromosome Inversions following Invasion of an Insect

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

Asymmetrical evolution of promoter methylation of mammalian genes after duplication

A Major Mitochondrial Gene Rearrangement Among Closely Related Species

SLC2A12of SLC2 Gene Family in Bird Provides Functional Compensation for the Loss ofSLC2A4Gene in Other Vertebrates

Navigating a fine balance: point-mutant cheater viruses disrupt the viral replication cycle

Co-evolution and Gene Transfers Drive Speciation Patterns in Host-Associated Bacteria

Less, but more: new insights from appendicularians on chordate Fgf evolution and the divergence of tunicate lifestyles

Asymmetrical evolution of promoter methylation of mammalian genes after duplication

Circadian rhythm mechanisms underlying convergent adaptation of unihemispheric slow-wave sleep in marine mammals