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

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

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

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

<i>SLC2A12</i>of SLC2 Gene Family in Bird Provides Functional Compensation for the Loss of<i>SLC2A4</i>Gene in Other Vertebrates

Abstract Bats are considered natural hosts for numerous viruses. Their ability to carry viruses that cause severe diseases or even death in other mammals without falling ill themselves has attracted widespread research attention. Toll-like receptor 2 (TLR2) forms heterodimers with TLR1 or TLR6 on cell membranes, recognizing specific pathogen-associated molecular patterns and playing a key role in innate immune responses. Previous studies have shown that moderate TLR2-mediated immune signals aid in pathogen clearance, while excessive or inappropriate TLR2-mediated immune signals can cause self-damage. In this study, we observed that TLR2, unlike TLR1 or TLR6, has undergone relaxed selection in bats compared to other mammals, indicating a reduced functional constraint on TLR2 specifically in bats. Indeed, our cell-based functional assays demonstrated that the ability of TLR2 to bind with TLR1 or TLR6 was significantly reduced in bats, leading to dampened inflammatory signaling. We identified mutations unique to bats that were responsible for this observation. Additionally, we found that mutations at residues 375 and 376 of TLR2 in the common ancestor of bats also resulted in reduced inflammatory response, suggesting that this reduction occurred early in bat evolution. Together, our study reveals that the TLR2-mediated inflammatory response has been specifically dampened in bats, which may be one of the reasons why they could harbor many viruses without falling ill.

Jiaming Zeng

Xiangyi Zhang

Chen Huang

Shilin Tian

Huabin Zhao

Dampened TLR2-mediated inflammatory signaling in bats

蝙蝠中抑制的TLR2介导的炎症信号传导

Abstract For a long time, snakes were presented as a textbook example of a group with gradual differentiation of homologous ZZ/ZW sex chromosomes. However, recent advances revealed that the ZZ/ZW sex chromosomes characterize only caenophidian snakes and certain species of boas and pythons have non-homologous XX/XY sex chromosomes. We used genome coverage analysis in four non-caenophidian species to identify their sex chromosomes, and we examined the homology of sex chromosomes across phylogenetically-informative snake lineages. We identified sex chromosomes for the first time in 13 species of non-caenophidian snakes, providing much deeper insights into the evolutionary history of snake sex chromosomes. The evolution of sex chromosomes in snakes is more complex than previously thought. Snakes may have had ancestral XX/XY sex chromosomes, which are still present in a blind snake and some boas, and there were several transitions to derived XX/XY sex chromosomes with different gene content and two or even three transitions to ZZ/ZW sex chromosomes. However, we discuss more alternative scenarios. In any case, we document that (1) some genomic regions were likely repeatedly co-opted as sex chromosomes in phylogenetically distant lineages, even with opposite types of heterogamety; (2) snake lineages differ greatly in the rate of differentiation of sex chromosomes; (3) snakes likely originally possessed sex chromosomes prone to turnovers. The sex chromosomes became evolutionarily highly stable once their differentiation progressed in the megadiverse caenophidian snakes. Snakes thus provide an ideal system for studying the evolutionary factors that drive unequal rates of differentiation, turnovers and stability of sex chromosomes.

Tomáš Pšenička

Barbora Augstenová

Daniel Frynta

Panagiotis Kornilios

Lukáš Kratochvíl

Michail Rovatsos

Sex chromosome turnovers and stability in snakes

蛇类性染色体的更替与稳定性

Abstract Pangenomes can facilitate a deeper understanding of genome complexity. Using de novo phased long-read assemblies of eight representative goat breeds, we constructed a graph-based pangenome of goats (Capra hircus) and discovered 113 Mb autosomal novel sequences. Combining this multi-assembly pangenome with low-coverage PacBio HiFi sequences, we constructed a long-read structural variations (SVs) database containing 59,325 SV deletions, 84,910 SV insertions and 24,954 other complex SV alleles. This resource allowed reliable graph-based genotyping from short reads of 79 wild and 1,148 worldwide domestic goats. Selection signal analysis of SV captured a novel immune-related domestication locus containing the galectin-9 gene and extra copies of the ruminant-specific galectin-9-like genes (LGALS9L), which have high tissue specificity. A segmental duplication in domestic goats generates three additional LGALS9L copies. Ancient goat genome sequences show a gradual increase in frequency of this duplication from the Neolithic to the present. Two other newly detected SVs also have higher selection signals than adjacent SNPs, a truncated-LINE1 deletion in EDAR2 associated with cashmere production and a VNTR-related insertion in PAPSS2 linked to high-altitude adaptation. In summary, the multi-assembly goat pangenome and long-read SV database facilitates detecting complex variations that are important in evolution and selection.

Peipei Bian

Jiaxin Li

Shishuo Zhou

Xingquan Wang

Mian Gong

Xi Guo

Yudong Cai

Qimeng Yang

Jiaqi Fu

Rongrong Li

Shuhong Huang

Funong Luo

Ali Mujtaba Shah

Johannes A Lenstra

Joram M Mwacharo

Ran Li

Gang Ren

Xiaolong Wang

Cong Li

Wenxin Zheng

Yu Jiang

Xihong Wang

A graph-based goat pangenome reveals structural variations involved in domestication and adaptation

基于图谱的山羊泛基因组揭示与驯化和适应相关的结构变异

Abstract Understanding metabolic plasticity of animal evolution is a fundamental challenge in evolutionary biology. Owing to the diversification of insect wing morphology and dynamic energy requirements, the molecular adaptation mechanisms underlying the metabolic pathways in wing evolution remain largely unknown. This study reveals the pivotal role of the duplicated Apolipoprotein D (ApoD) gene in lipid and energy homeostasis in the lepidopteran wing. ApoD underwent significant expansion in insects, with gene duplication and consistent retention observed in Lepidoptera. Notably, duplicated ApoD2 was highly expressed in lepidopteran wings and encoded a unique C-terminal tail, conferring distinct ligand-binding properties. Using Bombyx mori as a model organism, we integrated evolutionary analysis, multiomics, and in vivo functional experiments to elucidate the way duplicated ApoD2 mediates lipid trafficking and homeostasis via the AMP-activated protein kinase pathway in wings. Moreover, we revealed the specific expression and functional divergence of duplicated ApoD as a key mechanism regulating lipid homeostasis in the lepidopteran wing. These findings highlight an evolutionary scenario in which neofunctionalization conferred a novel role of ApoD in shaping adaptive lipid metabolic regulatory networks during wing phenotypic evolution. Overall, we provide in vivo evidence for the functional differentiation of duplicate genes in shaping adaptive metabolic regulatory networks during phenotypic evolution.

Shunze Jia

Rongqiao Li

Yinghui Li

Yuxin Huang

Minmin Liu

Yanyan Zhou

Yanting Liang

Zhihua Hao

Yusong Xu

Huabing Wang

Evolutionary novelty of Apolipoprotein D facilitates metabolic plasticity in lepidopteran wings

Apolipoprotein D的进化新特性促进鳞翅目昆虫翅膀的代谢可塑性

短名	Mol Biol Evol
Journal Impact	11.08
国际分区	GENETICS & HEREDITY(Q1)
期刊索引	SCI Q1中科院 1 区

ISSN	0737-4038, 1537-1719
h-index	245
国内分区	生物学(1区)生物学遗传学(1区)生物学生化与分子生物学(2区)生物学进化生物学(2区)
Top 期刊	是

涉及主题	生物遗传学化学生物化学基因进化生物学基因组医学系统发育树系统发育学社会学生态学人口学环境卫生人口地质学古生物学计算机科学
出版信息	出版商: Oxford University Press，出版周期: Monthly，期刊类型: journal，开源期刊: 是
基本数据	创刊年份: 1983，原创研究文献占比: 99.25%，自引率:2.70%， Gold OA占比: 95.42%
期刊费用	$3255详情
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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

Asymmetrical evolution of promoter methylation of mammalian genes after duplication

Dampened TLR2-mediated inflammatory signaling in bats

Sex chromosome turnovers and stability in snakes

A graph-based goat pangenome reveals structural variations involved in domestication and adaptation

Evolutionary novelty of Apolipoprotein D facilitates metabolic plasticity in lepidopteran wings