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

Uncoupling protein 1 (UCP1) is an essential protein in the mitochondrial inner membrane that mediates nonshivering thermogenesis (NST) and plays an important role in thermoregulation and fat deposition. However, the relationship between the evolution of UCP1 and fat deposition in the blubber layer in cetaceans remains unclear. Here, frameshift mutations, premature termination, and relaxed selection pressure (ω = 0.9557, P < 0.05) were detected in UCP1 in cetaceans, suggesting that UCP1 was inactivated during cetacean evolution. By time estimation, it was found that the inactivation of UCP1 in cetaceans occurred between 53.1 and 50.2 Ma. However, combined with findings from immunohistochemical analysis of the blubber layer of the Yangtze finless porpoise and in vitro functional assays, a premature termination of cetacean UCP1 resulted in a reduction of UCP1-mediated NST capacity (about 50%) and lipolytic capacity (about 40%), both of which were beneficial to maintain blubber layer and body temperature without excessive fat consumption. This study provides new insights into the molecular mechanisms of the blubber thickening in cetaceans and highlights the importance of UCP1 attenuation in cetaceans for secondary aquatic adaptation.

Ming Zhou

Tianzhen Wu

Yue Chen

Shixia Xu

Guang Yang

Functional Attenuation of <i>UCP1</i> as the Potential Mechanism for a Thickened Blubber Layer in Cetaceans

Abstract Photic niche shifts of mammals are associated with changing visual capabilities, primarily mediated by three visual pigments, two (SWS1 and M/LWS) of them for color vision and rhodopsin (RH1) for dim-light vision. To further elucidate molecular mechanisms of mammalian visual adaptations to different light environments, a systematic study incorporating evolutionary analyses across diverse groups and in vitro assays have been carried out. Here, we collected gene sequences for the three opsins from 220 species covering all major mammalian clades. After screening for cone opsin gene losses, we estimated selective pressures on each of the three genes and compared the levels of selection experienced by species living in bright- and dim-light environments. SWS1 pigment is shown to experience accelerated evolution in species living in bright-light environments as has RH1 in aquatic cetaceans, indicating potential shifts for ecological adaptations. To further elucidate the functional mechanisms for these two pigments, we then carried out site-directed mutagenesis in representative taxa. For SWS1, violet and ultraviolet sensitivities in the pika and mouse are mainly affected by substitutions at the critical sites 86 and 93, which have strong epistatic interaction. For RH1, the phenotypic difference between the sperm whale and bovine sequences is largely contributed by a substitution at site 195, which could be critical for dim-light sensation for deep-diving species. Different evolutionary patterns for the visual pigments have been identified in mammals, which correspond to photic niches, although additional phenotypic assays are still required to fully explain the functional mechanisms.

Yulin Gai

Ran Tian

Fangnan Liu

Yuan Mu

Lei Shan

David M Irwin

Yang Liu

Diversified Mammalian Visual Adaptations to Bright- or Dim-Light Environments

Arylalkylamine N-acetyltransferase (AANAT) plays a crucial role in synchronizing internal biological functions to circadian and circannual changes. Generally speaking, only one copy of AANAT gene has been found in mammals, however, three independent duplications of this gene were detected in several cetartiodactyl lineages (i.e., Suidae, Hippopotamidae, and Pecora), which originated in the middle Eocene, a geological period characterized with the increased climate seasonality. Lineage-specific expansions of AANAT and the associated functional enhancement in these lineages strongly suggest an improvement in regulating photoperiodic response to adapt to seasonal climate changes. In contrast, independent inactivating mutations or deletions of the AANAT locus were identified in the four pineal-deficient clades (cetaceans, sirenians, xenarthrans, and pangolins). Loss of AANAT function in cetaceans and sirenians could disrupt the sleep-promoting effects of pineal melatonin, which might contribute to increasing wakefulness, adapting these clades to underwater sleep. The absence of AANAT and pineal glands in xenarthrans and pangolins may be associated with their body temperature maintenance. The present work demonstrates a far more complex and intriguing evolutionary pattern and functional diversity of mammalian AANAT genes than previously thought and provides further evidence for understanding AANAT evolution as driven by rhythmic adaptations in mammals.

Daiqing Yin

RuRu Zhou

Mengxin Yin

Gene Duplication and Loss of<i>AANAT</i>in Mammals Driven by Rhythmic Adaptations

Abstract As phylogenomic datasets have grown in size, researchers have developed new ways to measure biological variation and to assess statistical support for specific branches. Larger datasets have more sites and loci, and therefore less sampling variance. While we can more accurately measure the mean signal in these datasets, lower sampling variance is often reflected in uniformly high measures of branch support—such as the bootstrap and posterior probability—limiting their utility. Larger datasets have also revealed substantial biological variation in the topologies found across individual loci, such that the single species tree inferred by most phylogenetic methods represents a limited summary of the data for many purposes. In contrast to measures of statistical support, the degree of underlying topological variation among loci should be approximately constant regardless of the size of the dataset. “Concordance factors” and similar statistics have therefore become increasingly important tools in phylogenetics. In this review, we explain why concordance factors should be thought of as descriptors of topological variation rather than as measures of statistical support, and argue that they provide important information about the predictive power of the species tree not contained in measures of support. We review a growing suite of statistics for measuring concordance, compare them in a common framework that reveals their interrelationships, and demonstrate how to calculate them using an example from birds. We also discuss how measures of topological variation might change in the future as we move beyond estimating a single “tree of life” towards estimating the myriad evolutionary histories underlying genomic variation.

Robert Lanfear

Matthew W Hahn

The meaning and measure of concordance factors in phylogenomics

系统发生基因组学中一致性因子的意义与测量

We propose an improved version of the neighbor-joining (NJ) algorithm of Saitou and Nei. This new algorithm, BIONJ, follows the same agglomerative scheme as NJ, which consists of iteratively picking a pair of taxa, creating a new mode which represents the cluster of these taxa, and reducing the distance matrix by replacing both taxa by this node. Moreover, BIONJ uses a simple first-order model of the variances and covariances of evolutionary distance estimates. This model is well adapted when these estimates are obtained from aligned sequences. At each step it permits the selection, from the class of admissible reductions, of the reduction which minimizes the variance of the new distance matrix. In this way, we obtain better estimates to choose the pair of taxa to be agglomerated during the next steps. Moreover, in comparison with NJ's estimates, these estimates become better and better as the algorithm proceeds. BIONJ retains the good properties of NJ--especially its low run time. Computer simulations have been performed with 12-taxon model trees to determine BIONJ's efficiency. When the substitution rates are low (maximum pairwise divergence approximately 0.1 substitutions per site) or when they are constant among lineages, BIONJ is only slightly better than NJ. When the substitution rates are higher and vary among lineages,BIONJ clearly has better topological accuracy. In the latter case, for the model trees and the conditions of evolution tested, the topological error reduction is on the average around 20%. With highly-varying-rate trees and with high substitution rates (maximum pairwise divergence approximately 1.0 substitutions per site), the error reduction may even rise above 50%, while the probability of finding the correct tree may be augmented by as much as 15%.

O Gascuel

BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data

Abstract Rates of molecular evolution vary greatly among even closely related species. Although theory predicts that antagonistic interactions between species increase rates of molecular evolution, predictions for how mutualism affects evolutionary rates are mixed. We compared rates of molecular evolution between 1) mutualistic and non-mutualistic legumes, 2) an independent set of symbiotic rhizobia and their non-symbiotic close relatives, and 3) symbiotic and non-symbiotic clades within Ensifer, a diverse genus of bacteria with various lifestyles. We assembled transcriptomes de novo for 12 legume species and calculated dN/dS ratios at orthologous genes in all species to determine if genes in mutualistic plants evolve faster or slower than in their non-mutualistic relatives. We also calculated dN/dS ratios in genes known to be important for symbiosis. We found that mutualists have higher rates of molecular evolution genome-wide compared to non-mutualist legumes, but this pattern did not hold in symbiosis genes. We next calculated dN/dS ratios in 14 bacteria species across the proteobacteria phylogeny that differ in whether they associate mutualistically with plants, using published data. In most pairs, symbiotic rhizobia show higher dN/dS values compared to their non-symbiotic relatives. Within a bacterial genus with many well-characterized mutualist species (Ensifer), we calculated dN/dS ratios in symbiotic and non-symbiotic clades and found that symbiotic lineages have higher rates of molecular evolution genome-wide, but not at genes on the symbiotic plasmid pSymB. Our results suggest that although mutualism between legumes and rhizobia is associated with elevated rates of molecular evolution genome-wide, symbiosis genes may be evolutionarily stagnant.

T L Harrison

J R Stinchcombe

M E Frederickson

Elevated rates of molecular evolution genome-wide in mutualist legumes and rhizobia

互惠豆科植物和根瘤菌基因组范围内分子进化率升高

Abstract In recent years, advances in image processing and machine learning have fueled a paradigm shift in detecting genomic regions under natural selection. Early machine learning techniques employed population-genetic summary statistics as features, which focus on specific genomic patterns expected by adaptive and neutral processes. Though such engineered features are important when training data is limited, the ease at which simulated data can now be generated has led to the recent development of approaches that take in image representations of haplotype alignments and automatically extract important features using convolutional neural networks. Digital image processing methods termed α-molecules are a class of techniques for multi-scale representation of objects that can extract a diverse set of features from images. One such α-molecule method, termed wavelet decomposition, lends greater control over high-frequency components of images. Another α-molecule method, termed curvelet decomposition, is an extension of the wavelet concept that considers events occurring along curves within images. We show that application of these α-molecule techniques to extract features from image representations of haplotype alignments yield high true positive rate and accuracy to detect hard and soft selective sweep signatures from genomic data with both linear and nonlinear machine learning classifiers. Moreover, we find that such models are easy to visualize and interpret, with performance rivaling those of contemporary deep learning approaches for detecting sweeps.

Md Ruhul Amin

Mahmudul Hasan

Michael DeGiorgio

Digital image processing to detect adaptive evolution

数字图像处理用于检测适应性进化

Abstract Genes encoded within organelle genomes often evolve at rates different from those in the nuclear genome. Here, we analyzed the relative rates of nucleotide substitution in the mitochondrial, apicoplast and nuclear genomes in four different lineages of Plasmodium species (malaria parasites) infecting mammals. The rates of substitution in the three genomes exhibit substantial variation among lineages, with the relative rates of nuclear and mitochondrial DNA being particularly divergent between the Laverania (including Plasmodium falciparum) and Vivax lineages (including Plasmodium vivax). Consideration of synonymous and nonsynonymous substitution rates suggests that their variation is largely due to changes in mutation rates, with constraints on amino acid replacements remaining more similar among lineages. Mitochondrial DNA mutation rate variations among lineages may reflect differences in the long-term average lengths of the sexual and asexual stages of the life cycle. These rate variations have far-reaching implications for the use of molecular clocks to date Plasmodium evolution.

Hend Abu-Elmakarem

Oscar A MacLean

Frank Venter

Lindsey J Plenderleith

Richard L Culleton

Beatrice H Hahn

Paul M Sharp

Remarkable evolutionary rate variations among lineages and among genome compartments in malaria parasites of mammals

哺乳动物疟原虫在谱系间和基因组区间内显著的进化速率变异

Abstract Multiple rounds of whole-genome duplication (WGD) followed by diploidization have occurred throughout the evolutionary history of angiosperms. Much work has been done to model the genomic consequences and evolutionary significance of WGD. While researchers have historically modeled polyploids as either allopolyploids or autopolyploids, the variety of natural polyploids span a continuum of differentiation across multiple parameters, such as the extent of polysomic vs. disomic inheritance, and the degree of genetic differentiation between the ancestral lineages. Here we present a forward-time polyploid genome evolution simulator called SpecKS. SpecKS models polyploid speciation as originating from a 2D continuum, whose dimensions account for both the level of genetic differentiation between the ancestral parental genomes, as well the time lag between ancestral speciation and their subsequent reunion in the derived polyploid. Using extensive simulations, we demonstrate that changes in initial conditions along either dimension of the 2D continuum deterministically affect the shape of the Ks histogram. Our findings indicate that the error in the common method of estimating WGD time from the Ks histogram peak scales with the degree of allopolyploidy, and we present an alternative, accurate estimation method that is independent of the degree of allopolyploidy. Lastly, we use SpecKS to derive tests that infer both the lag time between parental divergence and WGD time, and the diversity of the ancestral species, from an input Ks histogram. We apply the latter test to transcriptomic data from over 200 species across the plant kingdom, the results of which are concordant with the prevailing theory that the majority of angiosperm lineages are derived from diverse parental genomes and may be of allopolyploid origin.

Tamsen Dunn

Arun Sethuraman

Accurate Inference of the Polyploid Continuum using Forward-time Simulations

使用向前时间模拟精确推断多倍体连续体

Abstract The evolution of sex chromosomes can involve recombination suppression sometimes involving structural changes, such as inversions, allowing subsequent rearrangements, including inversions and gene transpositions. In the two major genus Salix clades, Salix and Vetrix, almost all species are dioecious, and sex-linked regions have evolved on chromosome 7 and 15, with either male or female heterogamety. We used chromosome conformation capture (Hi-C) and PacBio HiFi (high-fidelity) reads to assemble chromosome-level, gap-free X and Y chromosomes from both clades, S. triandra (15XY system), a basal species in the Vetrix clade, and the Salix clade species S. mesnyi (7XY system). Combining these with other available genome assemblies, we found inversions within the sex-linked regions, which are likely to be pericentromeric and probably recombined rarely in the ancestral species, before sex-linkage evolved. The Y-linked regions in all 15XY and 7XY species include partial duplicates containing exon 1 of an ARR17-like gene similar to male-determining factors in other Salicaceae species. We also found duplicates of a Y-specific gene, which we named MSF. The derived Salix clade 7XY chromosome systems appear to have evolved when these two genes transposed from the 15Y to the 7Y. Additionally, the 7Y chromosomes in S. dunnii and S. chaenomeloides probably evolved from the ancestral 7X of the Salix clade, involving a similar transposition, and loss of the ancestral 7Y. We suggest that pericentromeric regions that recombine infrequently may facilitate the evolution of sex-linkage.

Yi Wang

Ren-Gang Zhang

Elvira Hörandl

Zhi-Xiang Zhang

Deborah Charlesworth

Li He

Evolution of sex-linked genes and the role of pericentromeric regions in sex chromosomes: insights from diploid willows

性连锁基因的演化及着丝粒周边区域在性染色体中的作用：二倍体柳树的启示

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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Functional Attenuation of UCP1 as the Potential Mechanism for a Thickened Blubber Layer in Cetaceans