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Current understanding of the adaptive evolution of the SARS-CoV-2 genome.
Q3 Medicine Pub Date : 2025-02-01 DOI: 10.16288/j.yczz.24-231
Lin Zhang, Zhuo-Cheng Yao, Jian Lu, Xiao-Lu Tang

The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has significantly impacted human life safety and the global economy. The rapid mutation of the SARS-CoV-2 genome has attracted widespread attention, with almost every site in the genome experiencing single nucleotide variants (SNVs). Among these, the mutations in the spike (S) protein are of particular importance, as they play a more critical role in the virus's adaptive evolution and transmission. In this review, we summarize the phylogenetic relationships between SARS-CoV-2 and related coronaviruses in non-human animals, and delves into the lineage classification of SARS-CoV-2 and the impact of key amino acid variations on viral biological characteristics. Furthermore, it outlines the current challenges and looks forward to the promising application of deep mutational scanning (DMS) combined with artificial intelligence methods in predicting the prevalence trends of SARS-CoV-2 variants.

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引用次数: 0
Evolution by gene duplication: in the era of genomics.
Q3 Medicine Pub Date : 2025-02-01 DOI: 10.16288/j.yczz.24-215
Jie-Yu Shen, Tian-Han Su, Da-Qi Yu, Sheng-Jun Tan, Yong-E Zhang

Gene duplication is the process of a gene copied via specific molecular mechanisms to form more duplicate genes. As an important approach to the origination of new genes, gene duplication contributes to around half of the genes in eukaryotic genomes, facilitating the adaptive evolution of species. Over the past fifty years, especially since entering the genomics era in the last two decades, there have been extensive and profound discussions on the mechanisms, evolutionary processes and forces behind the emergence of duplicate genes. Sequence similarity of duplicate genes often leads to functional redundancy, enhancing organismal robustness. Conversely, functional divergence can create novel functions and improve evolvability. In this review, we summarize the mechanism of gene duplication, the fate and the evolutionary models of duplicate genes. This article concludes by outlining how long-read sequencing technologies, gene editing, and various other high-throughput techniques will further advance our understanding of the role of duplicate genes in the genetics-development-evolution network.

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引用次数: 0
Theoretical thinking from gene evolution to cell type evolution.
Q3 Medicine Pub Date : 2025-02-01 DOI: 10.16288/j.yczz.24-148
Li Zhang, Chuan-Yun Li

During evolution, mutations occur randomly and are fixed by selection. At the same time, species gradually formed, producing various life forms. In the traditional evolutionary theory system, mutations are considered genetic mutations by default, and somatic mutations are usually applicable in specific scenarios such as carcinogenesis, immunity and aging. At the same time, selection plays a role at multiple levels of living systems, including genes, cells, tissues and organs, individuals, populations, species, and even ecosystems. The research community of modern life science expresses genetic mutations as genotypes and cellular and other level characteristics as phenotypes, and finds that phenotypes are determined by both genotypes and environmental factors. Currently, it is unclear how genotypic and environmental factors act at the cellular level to create and fix new cell types. In this review, we summarize that it's time to move forward from gene evolution to build the framework for cell type evolution and finally update the theoretical system for evolutionary biology.

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引用次数: 0
Evolutionary ecology in tumor evolution: concept, application and innovation.
Q3 Medicine Pub Date : 2025-02-01 DOI: 10.16288/j.yczz.24-264
Can Liu, Wei-Wei Zhai, Xue-Mei Lu

Tumor itself is a complex microecosystem, with complex spatio-temporal dynamics and multi-dimensional interactions. Its unimaginable heterogeneity and evolvability have exceeded the cognition of traditional oncology medicine. How to systematically characterize the whole tumor cell ecosystem from the dynamics and interaction of material, energy and signal levels, in order to explore new cognition, new rules and new therapies for the occurrence and development of tumors, is a new proposition and goal of tumor ecology. In this review, we discuss the origin, occurrence and development of tumors from the perspective of evolutionary ecology. First, we discuss the application of some classical concepts of ecology with tumor evolution. Subsequently, through the integration of the frontier papers of tumor ecology, we highlight the importance of ecological interactions on the occurrence and development of tumors from multiple levels, such as between cancer cells, between cancer cells and other normal somatic cells, and the tumor ecosystem. Finally, we propose the concept of tumor cell ecosystem, discussed how to characterize the entire tumor ecosystem from the system theory and proposed possible innovative treatment directions.

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引用次数: 0
Advances in vocalizating and hearing mechanisms of echolocation in vertebrate.
Q3 Medicine Pub Date : 2025-02-01 DOI: 10.16288/j.yczz.24-273
Qi Liu, Peng Shi

Echolocation is a complex biological traits that collaborated by multiple systems. Its origin can be traced back to 68 million years ago, and repeatedly appeared in multiple vertebrate groups in the subsequent biological evolution. The strong vitality has become a typical case of the convergence evolution in nature. However, it was not until the beginning of the 20th century that humans really opened the prelude to the research on animal echolocation, and became research hotspots in the fields of zoology, behavior, and genetics, and achieved rich results in the past 80 years. In this review, we summarize the development history of animal echo positioning, summarize different echo positioning animal groups in detail, and focuse on the research progress of echo positioning in sound mechanisms, acoustic characteristics, and high-frequency listening mechanisms in order to provide reference for comprehensive understanding of animal echo positioning.

回声定位是一种由多个系统协同作用的复杂生物特征。它的起源可以追溯到6800万年前,并在随后的生物进化中反复出现在多个脊椎动物类群中。强大的生命力成为自然界趋同进化的典型案例。然而,直到20世纪初,人类才真正拉开了动物回声定位研究的序幕,并成为动物学、行为学、遗传学等领域的研究热点,在近80年的时间里取得了丰富的成果。在这篇综述中,我们总结了动物回声定位的发展历程,详细归纳了不同的回声定位动物群体,并重点介绍了回声定位在声机制、声学特性和高频听觉机制等方面的研究进展,以期为全面了解动物回声定位提供参考。
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引用次数: 0
Dosage compensation of sex chromosomes in animals.
Q3 Medicine Pub Date : 2025-02-01 DOI: 10.16288/j.yczz.24-165
Xiao-Shu Chen, Jia-Bi Chen

The origin and evolution of sex chromosomes have long been a focus of research in biology. Two of the most studied systems are the XY system and the ZW system. Due to Y/W degeneration, heterozygous (XY/ZW) sex-linked genes are absent and their dosage is reduced when compared to autosomal genes and homozygous (XX/ZZ) sex-linked genes, creating an issue of dosage imbalance between sex chromosomes and autosomes. Multiple evolutionary models have been proposed to explain the evolutionary mechanism of dosage compensation that might resolve such dosage imbalance. In this review, we summarize the findings related to the dosage effect of sex chromosomes from a variety of perspectives, including transcriptomes, proteomes, haploid cells, and single cells. In addition, a summary of the dosage effect of sex chromosomes in major phylogenetic branches of multiple species is provided. Finally, we approved an overview of the related theoretical models and future research directions at the end of this paper.

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引用次数: 0
Progress and prospects on evolutionary developmental biology of butterfly wing patterns.
Q3 Medicine Pub Date : 2025-02-01 DOI: 10.16288/j.yczz.24-126
Jia-Xin Ni, Wei Zhang

Evolutionary developmental biology combines evolutionary biology and developmental biology, focusing on the evolution of developmental processes and the mechanisms of morphological diversification. Since the discovery of the homeobox gene in 1984, the genetic mechanisms of morphogenesis in multiple model organisms have been systematically studied. In contrast, non-model organisms are rich in complex evolutionary traits, yet their underlying genetic mechanisms have not yet been fully elucidated, so more relevant studies are still needed. Among non-model organisms, butterflies are rich in species diversity, with more than 18,700 species. In particular, butterfly wings have simple flat structures but exhibit diverse and complex patterns, likely associated with complex functions(e.g., defense and courtship) and subject to strong selective pressures, which makes them a classic system for evolutionary developmental biology studies. Early comparative morphological studies proposed the Nymphalid ground plan, providing a theoretical framework for the evolutionary developmental biology of butterfly wing patterns; a series of interference experiments on butterfly wing discs later confirmed the association between the wing developmental process and phenotypes. In recent years, by integrating genetics, developmental biology, and genomics research methods, genetic toolkit genes and loci involved in wing pattern regulation have been identified in several butterfly species, further improving the theoretical framework for studying butterfly wing pattern evolution and development. From the methodological perspective, experimental methods such as in situ hybridization and gene editing have played an important role in evolutionary developmental biology studies of butterfly wings, and the development of hybridization chain reaction technology and CRISPR/Cas9 gene editing technology has further advanced the feasibility of functional validation in butterflies. In the future, the development and optimization of lepidopteran RNA interference and gene editing technologies can promote functional studies, thus expanding the research systems of evolutionary developmental biology by comparing and analyzing complex traits. The above research can also be broadened to an ecological-evolutionary-developmental context to explore genetic and environmental factors that shape complex phenotypes(e.g., butterfly wing patterns), thereby deepening the understanding of key scientific issues such as the origin and evolution of biodiversity.

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引用次数: 0
Why should we stop translating "evolution" to "" and turn to use "" in Chinese. 为什么我们要停止把“进化”翻译成“”而改用中文的“”呢?
Q3 Medicine Pub Date : 2025-01-01 DOI: 10.16288/j.yczz.24-194
Zhong-Yi Sun, Guo-Jie Zhang
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引用次数: 0
Speciation studies in the genomic era. 基因组时代的物种形成研究。
Q3 Medicine Pub Date : 2025-01-01 DOI: 10.16288/j.yczz.24-218
Ze-Fu Wang, Jian-Quan Liu

Since Darwin's era, speciation has been one of the most central issues in evolutionary biology studies. Understanding the processes of species origin is crucial in deepening our understanding of the formation of species biodiversity, which is essential for their protections. However, speciation research has been challenging due to the rather complex evolutionary histories of many extant species. In recent years, with the continuous advancements in genomic sequencing techniques, significant advances have been achieved in the field of speciation researches. In this review, we overview speciation study advances, especially in the concepts and latest developments in research methods for studying speciation in the genomic era, encompassing the major research aspects: species delimitation, bifurcating speciation, hybrid speciation, polyploid speciation, reproductive isolation genes and speciation genes. Furthermore, we discuss the limitations of these studies and methods. Finally, we provide the outlook on the future challenges and directions in speciation researches.

自达尔文时代以来,物种形成一直是进化生物学研究中最核心的问题之一。了解物种起源的过程对于加深我们对物种生物多样性形成的理解至关重要,这对物种的保护至关重要。然而,由于许多现存物种的进化历史相当复杂,物种形成研究一直具有挑战性。近年来,随着基因组测序技术的不断进步,物种形成研究领域取得了重大进展。本文综述了基因组时代物种形成研究的概念和研究方法的最新进展,主要包括物种划分、分叉物种形成、杂交物种形成、多倍体物种形成、生殖隔离基因和物种形成基因。此外,我们还讨论了这些研究和方法的局限性。最后,对未来物种形成研究的挑战和方向进行了展望。
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引用次数: 0
The migration and evolutionary mechanisms of northern Asian populations from the perspective of ancient genomics. 古代基因组学视角下的北亚种群迁移和进化机制。
Q3 Medicine Pub Date : 2025-01-01 DOI: 10.16288/j.yczz.24-196
Da-Xuan Zhang, Shen-Ru Dai, Yin-Qiu Cui

The northern part of Asia, including Siberia, the Mongolian Plateau, and northern China, is not only a crossroads for population exchange on the Eurasian continent but also an important bridge connecting the American continent. This region holds a unique and irreplaceable significance in exploring the origins of humanity, tracking human migration routes, and elucidating evolutionary mechanisms. Despite the limited number of samples unearthed, varying preservation conditions, and constraints of technical means, our understanding of the interactions among populations in northern Asia is still in its infancy. However, the development of high-throughput sequencing technology and its advancement in ancient DNA research have provided us with a new perspective for delving into the genetic history of ancient populations from a molecular level. In this review, we synthesize the changes in the genetic structure of ancient populations in different stages of northern Asia, aiming to reveal the patterns of interaction among ancient populations in this region, the evolutionary process of their genetic structure, and their genetic contributions to modern populations. It will also discuss the adaptive strategies of humans in response to extreme natural conditions. This will not only deepen our understanding of the origins and migration processes of humanity but also provide a solid foundation for studying the evolutionary mechanisms and adaptive strategies of humans under environmental selective pressures.

包括西伯利亚、蒙古高原和中国北部在内的亚洲北部地区,不仅是欧亚大陆人口交流的十字路口,也是连接美洲大陆的重要桥梁。该地区在探索人类起源、追踪人类迁徙路线、阐明进化机制等方面具有独特而不可替代的意义。尽管出土样本数量有限,保存条件各异,技术手段有限,但我们对北亚种群间相互作用的理解仍处于起步阶段。然而,高通量测序技术的发展及其在古代DNA研究中的进展,为我们从分子水平深入研究古代人群的遗传历史提供了新的视角。本文综合分析了北亚不同时期古代居群遗传结构的变化,旨在揭示该地区古代居群间的相互作用模式、遗传结构的演化过程及其对现代居群的遗传贡献。它还将讨论人类对极端自然条件的适应策略。这不仅加深了我们对人类起源和迁移过程的认识,而且为研究人类在环境选择压力下的进化机制和适应策略提供了坚实的基础。
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