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地理基因组学：研究方法与进展

虎灵1,2, 沈泽昊3,2*   

  1. 1. 云南大学国际河流与生态安全研究院, 昆明 650500; 2. 西南联合研究生院, 昆明 650092; 3. 北京大学城市与环境学院，地表过程分析与模拟教育部重点实验室，北京 100871
  • 收稿日期:2025-01-10 修回日期:2025-03-06 接受日期:2025-05-12
  • 通讯作者: 沈泽昊

Geogenomics: Research methods and advances

Ling Hu1,2, Zehao Shen3,2*   

  1. 1 Institute of International Rivers and Eco-security, Yunnan University, Kunming 650500, China 

    2 Southwest United Graduate Schools, Kunming 650092, China 

    3 College of Urban and Environmental Sciences, Key Laboratory of Ministry of Education for Earth Surface Processes, Peking University, Beijing 100871, Chin

  • Received:2025-01-10 Revised:2025-03-06 Accepted:2025-05-12
  • Contact: Zehao Shen

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摘要： 随着地球科学与生命科学的融合发展，由地质学、地貌学、古气候学、基因组学、系统发育学、种群遗传学和生物地理学等多学科关联形成的地理基因组学（geogenomics）将地表景观变化与生物演化联系起来，成为检验地质假设、重建地球历史及其生物协同演化的一个有效途径，并在全球生态保护方面展现出巨大潜力。本文系统介绍了地理基因组学的基础概念和关键科学问题，及其与相关研究领域的关系，并通过Web of Science核心数据库的文献检索和计量，分析了地理基因组学的研究主题演变和热点演变。作为一门正在兴起的多学科交叉领域，地理基因组学深度整合地质、气候和基因组数据，反演地质构造运动、生物类群分化历史和分布变迁的时空格局和相互影响，对促进地质学和生物进化研究具有重要意义。本文重点关注五个研究内容：检验地质假说；阐明区域或洲际尺度的地质过程；推断区域多样性演化历史；地质重建中的不确定性与尺度效应，以及病原体的地理分布模式和扩散起源。目前，我国在这一领域的相关研究还非常有限，但已针对若干重要科学问题展开，如青藏高原的差异性隆升历史，长江黄河水系的演变等。未来还应进一步加强多学科方法的应用，开发更好的工具，并推动建立全球地理基因组学研究数据库。

关键词: 地理基因组学, 物种演化, 地质过程, 假说, 跨学科, 高通量测序

Abstract

Background & Aims: With the integrated development of earth sciences and life sciences. geogenomics—an interdisciplinary field integrating geology, geomorphology, geomorphology, paleoclimatology, genomics, phylogenetics, population genetics, and biogeography—links surface landscape changes to biological evolution. This field has become an effective way for testing geological hypotheses and reconstructing Earth’s history, as well as exploring its co-evolution with life. Geogenomics also shows significant potential in global ecological conservation. 

Methods: In this review, we systematically introduce the fundamental concepts and key scientific questions of geogenomics, as well as its relationship to related research fields. We retrieved the Web of Science core collection, and analyze the evolution of themes and hotspots in geogenomics through bibliometric analysis. 

Review Results: As an emerging interdisciplinary field, geogenomics deeply integrates geological, climatic, and genomic data to inverts the spatio-temporal patterns and interactions between geological structure movements and the history and distribution changes of biological groups. This field holds significant promise for advancing geological and biological evolution. We focus on five key aspects: testing geological hypotheses; elucidating regional or intercontinental scale geological processes; inferring regional biodiversity evolution history; addressing uncertainties in geological reconstruction and scale effects, as well as the geographical distribution patterns and dispersal origins of pathogens. 

Perspectives: At present, research in this field is still limited in our country, but it has been carried out on several important scientific questions, such as the uplift history was highly variable of the Qinghai-Tibetan Plateau and the evolution of the Yangtze and Yellow River systems. In the future, it is imperative to enhance the application of multidisciplinary approaches, develop more effective tools, and advocate for the establishment of a global geogenomics research database.

Key words: geogenomics, species evolution, geological process, hypothesis, interdisciplinary, high-throughput sequencing

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