Geogenomics: Research methods and advances

doi:10.17520/biods.2025010

Abstract

Abstract:

Background & Aims: With the integrated development of earth sciences and life sciences, geogenomics—an interdisciplinary field integrating geology, 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 utilized the Web of Science core collection, and analyze the evolution of themes and hotspots in geogenomics through bibliometric analysis. Meanwhile, we systematically introduce the fundamental concepts and key scientific questions of geogenomics, as well as its relationship to related research fields.

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 China, 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 River 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

Ling Hu, Zehao Shen. Geogenomics: Research methods and advances[J]. Biodiv Sci, 2025, 33(7): 25010.

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URL: https://www.biodiversity-science.net/EN/10.17520/biods.2025010

https://www.biodiversity-science.net/EN/Y2025/V33/I7/25010

Figures/Tables 6

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聚类标签 Name	连接权重 Weight link	总连接强度权重 Weight total links strength	排名前5的关键词 Top 5 keywords
地理隔离 Vicariance	403	529	地理隔离; 系统发育; 多样化; 扩散; 特有性 Vicariance; phylogenetics; diversification; dispersal; endemic
物种形成 Speciation	363	438	物种形成; 生态位模型; 山脉; 群体遗传学; 溯祖理论 Speciation; ecological niche modeling; mountains; population genetics; coalescent
生物地理学 Biogeography	473	633	生物地理学; 基因流; 安第斯山脉隆升; 分化时间; 河流 Biogeography; gene flow; Andean uplift; divergence time; river
河流袭夺 River capture	348	506	河流袭夺; 冰期; 基因组; 动态历史; 基因渐渗 River capture; glaciations; genome; demographic history; introgression
谱系生物地理学 Phylogeography	389	764	谱系生物地理学; 避难所; 遗传多样性; 更新世; 陆桥 Phylogeography; refugia; genetic diversity; Pleistocene; land bridge
构造运动 Tectonic movement	196	239	构造运动; 遗传分化; 种群动态; 东亚; 古地理 Tectonic movement; genetic differentiation; population dynamics; East Asia; palaeogeography
线粒体DNA Mitochondrial DNA	241	338	线粒体DNA; 鱼; 古水系; 地貌演化; 海平面变化 Mitochondrial DNA; fish; Palaeodrainage; geomorphic evolution; sea-level changes
脱氧核糖核酸 DNA	260	441	脱氧核糖核酸; 叶绿体DNA; 第四纪气候; 遗传结构; 冰期避难所 DNA; chloroplast DNA; quaternary climate; genetic structure; glacial refugia
分子钟 Molecular clock	179	226	分子钟; 广泛分布; 系统发育基因组学; 贝叶斯分析; 古DNA Molecular clock; wide distribution; phylogenomic; Bayesian analyses; ancient DNA
喜马拉雅-横断山区 Himalaya-Hengduan Mountains	87	112	喜马拉雅-横断山区; 物种分布模型; 两栖动物; 水系演化; 环境变化 Himalaya-Hengduan Mountains; species distribution modeling; amphibians; drainage evolution; environmental changes
地质事件 Geological events	126	165	地质事件; 进化历史; 东南亚; 校准; 淡水 Geological events; evolutionary history; Southeast Asia; calibration; freshwater
气候变化 Climate change	121	171	气候变化; 青藏高原隆升; 墨西拿盐度危机; 特提斯海; 茜草科 Climate change; Qinghai-Tibetan Plateau uplift; Messinian salinity crisis; Tethys Sea; Rubiaceae

聚类标签 Name	连接权重 Weight link	总连接强度权重 Weight total links strength	排名前5的关键词 Top 5 keywords
地理隔离 Vicariance	403	529	地理隔离; 系统发育; 多样化; 扩散; 特有性 Vicariance; phylogenetics; diversification; dispersal; endemic
物种形成 Speciation	363	438	物种形成; 生态位模型; 山脉; 群体遗传学; 溯祖理论 Speciation; ecological niche modeling; mountains; population genetics; coalescent
生物地理学 Biogeography	473	633	生物地理学; 基因流; 安第斯山脉隆升; 分化时间; 河流 Biogeography; gene flow; Andean uplift; divergence time; river
河流袭夺 River capture	348	506	河流袭夺; 冰期; 基因组; 动态历史; 基因渐渗 River capture; glaciations; genome; demographic history; introgression
谱系生物地理学 Phylogeography	389	764	谱系生物地理学; 避难所; 遗传多样性; 更新世; 陆桥 Phylogeography; refugia; genetic diversity; Pleistocene; land bridge
构造运动 Tectonic movement	196	239	构造运动; 遗传分化; 种群动态; 东亚; 古地理 Tectonic movement; genetic differentiation; population dynamics; East Asia; palaeogeography
线粒体DNA Mitochondrial DNA	241	338	线粒体DNA; 鱼; 古水系; 地貌演化; 海平面变化 Mitochondrial DNA; fish; Palaeodrainage; geomorphic evolution; sea-level changes
脱氧核糖核酸 DNA	260	441	脱氧核糖核酸; 叶绿体DNA; 第四纪气候; 遗传结构; 冰期避难所 DNA; chloroplast DNA; quaternary climate; genetic structure; glacial refugia
分子钟 Molecular clock	179	226	分子钟; 广泛分布; 系统发育基因组学; 贝叶斯分析; 古DNA Molecular clock; wide distribution; phylogenomic; Bayesian analyses; ancient DNA
喜马拉雅-横断山区 Himalaya-Hengduan Mountains	87	112	喜马拉雅-横断山区; 物种分布模型; 两栖动物; 水系演化; 环境变化 Himalaya-Hengduan Mountains; species distribution modeling; amphibians; drainage evolution; environmental changes
地质事件 Geological events	126	165	地质事件; 进化历史; 东南亚; 校准; 淡水 Geological events; evolutionary history; Southeast Asia; calibration; freshwater
气候变化 Climate change	121	171	气候变化; 青藏高原隆升; 墨西拿盐度危机; 特提斯海; 茜草科 Climate change; Qinghai-Tibetan Plateau uplift; Messinian salinity crisis; Tethys Sea; Rubiaceae

学科 Disciplines	方法和数据 Methods and data	研究问题 Research question	时间尺度 Temporal scale (yr)^*	空间尺度 Spatial scale	应用 Applications	参考文献 References
谱系生物地理学 Phylogeography	方法: 系统发育重建; 谱系结构分析; 中性理论; 最大熵模型; 生态位模型; 谱系多样性; 区系相似性分析; 分子钟分析; 谱系扩散隔离分析等。数据: 分子遗传数据; 气候变化, 环境; 化石; 物种地理分布; 系统发育; 土地利用; 人类活动等。 Methods: Phylogenetic reconstruction; genetic structure analysis; neutral theory; maximum entropy model; ecological niche modeling; phylogenetic diversity; floral similarity analysis; molecular clock analysis; dispersal-vicariance analysis, etc. Data: Genetic data; climate change; environmental; fossil; geographical distribution of species; phylogeny; land use; human activities, etc.	谱系的地理分布和种群的进化历史等。 Geographic distribution of lineages; evolutionary history of populations	10³-10⁶	局部-区域 Local- regional	物种形成假说检验; 物种遗传多样性分析; 物种分化研究; 扩散和隔离分化研究等。 Speciation hypothesis testing; genetic diversity analysis of species; species differentiation; dispersal-vicariance -divergence, etc.	Emerson & Hewitt, 2005; Avise, 2009
景观遗传学 Landscape genetics	方法: Mantel检验; 遗传多样性估计; 结构方程模型; 最小成本路径分析; Monmonier最大差异算法; 回归分析; 距离隔离检验等。数据: 分子遗传; 环境变化; 土地利用; 人类活动等。 Methods: Mantel test; genetic diversity estimates; structural equation models; least cost paths analysis; Monmonier’s maximum difference algorithm; regression analysis; isolation-by-distance test, etc. Data: Genetic data; environmental change; land use; human activities, etc.	景观结构的遗传效应; 景观对基因流动的影响; 基于物种的时空尺度耦合等。 Genetic effects of landscape structure; influence of landscape on gene flow; spatio-temporal scale coupling based on species	10-10²	局部-区域 Local- regional	确定保护单元; 评估种群状况; 管理入侵物种; 种群恢复等。 Identification of conservation units; assessment of population status; management of invasive species; population recovery, etc.	Manel et al, 2003; Segelbacher et al, 2010; 沈泽昊和吉成均, 2010
保护遗传学 Conservation genetics	方法: 遗传多样性分析; 贝叶斯聚类分析; 物种分布模拟等。数据: 分子遗传数据; 物种分布数据等。 Methods: Genetic diversity analysis; Bayesian cluster analysis; species distribution modeling, etc. Data: Genetic data; geographical distribution of species, etc.	濒危物种保护; 遗传多样性保护; 保持物种进化潜力等。 Conservation of endangered species; conservation of genetic diversity; preservation of species’ evolutionary potential, etc.	10-10²	局部- 区域 Local- regional	评估种群结构; 确定物种保护单元; 保护管理对策制定等。 Population structure assessment; identification of species conservation units; formulation of conservation management strategies, etc.	Hedrick, 2001; 谭鑫鑫和李明, 2018
保护生物地理学 Conservation biogeography	方法: 物种丰富度和特有性分析; 遗传多样性估计; 空间多样性分析; GIS; 基因流分析; 敏感性分析; 网络分析; 物种分布模型; 生态位模型; 生物气候包络模型等。数据: 分子遗传; 物种分布数据; 遥感; 土地利用; 人类活动等。 Methods: Species richness and endemic analysis; genetic diversity estimates; spatial diversity analysis; GIS; gene flow; sensitivity analysis; network analysis; species distribution modeling; ecological niche modeling; bioclimate envelope modeling, etc. Data: Genetic data; geographical distribution of species; remote sensing; land use; human activities, etc.	生物多样性保护; 生态格局与过程的时空动态和保护决策等。 Biodiversity conservation; temporal and spatial dynamics of ecological patterns and processes and conservation decisions, etc.	10³-10⁶	区域- 全球 Regional- global	评估种群规模; 保护区规划; 物种分布模拟; 物种入侵模式和驱动因素分析; 自然保护区评估; 气候避难所的识别等。 Assessment of population size; protected area planning; species distribution modeling; species invasion patterns and driving factors analysis; assessment of nature reserve; identification of climate refuges, etc.	Whittaker et al, 2005; Richardson & Whittaker, 2010
生物地理学 Biogeography	方法: 空间自相关分析; 热点分析; Mantel检验; 贝叶斯分析; 遗传结构分析; 系统发育分析; 物种分布模型; 谱系地理格局分析; 物种扩散-灭绝模型; 生态位模型等。数据: 分子遗传; 遥感; 气候变化; 环境; 物种分布; 古气候; 化石; 土地利用; 人类活动等。 Methods: Spatial autocorrelation analysis; hotspot analysis; Mantel test; Bayesian analysis; genetic structure analysis; phylogenetic analysis; species distribution modeling; phylogeographical pattern analysis; dispersal-extinction analysis; ecological niche modeling, etc. Data: Genetic data; remote sensing; climate change; environmental; geographical distribution of species; paleoclimate; fossil; land use; human activities, etc.	现存物种的起源; 物种分布模式; 植物区系; 生物多样性保护等。 Origin of existing species; distribution patterns of species; flora; biodiversity conservation, etc.	10-10⁶	区域- 全球 Regional- global	植物区系划分; 山地植被与地理环境的关系; 物种起源扩散研究等。 Division of flora; the relationship between mountain vegetation and geographic environment; species origin and diffusion, etc.	McDowall, 2004; Wiens & Donoghue, 2004; Posadas et al, 2006
地理基因组学 Geogenomics	方法: 年代学分析; 岩相分析; 地球化学分析; 隔离屏障模拟分析; 系统发育分析; 遗传结构分析、基因流分析; 分化时间分析; 种群动态分析; 情景模拟分析; 一致性检验; 统计假设检验等。数据: 分子遗传; 物种分布数据; 遥感; 地质与历史事件; 地质年代; 沉积学; 古气候等。 Methods: Chronological analysis; petrographic analysis; geochemical analysis; dispersal- vicariance simulation analysis; phylogenetic analysis; genetic structure analysis; gene flow analysis; differentiation time analysis; population dynamics analysis; scenario simulation analysis; concordance test; statistical hypothesis testing, etc. Data: Genetic data; geographical distribution of species; remote sensing; geological and historical events; geologic age; sedimentary evidence; paleoclimate, etc.	检验地质假说; 阐明区域或洲际地质过程; 多样性历史分析; 地质重建中的不确定性与尺度效应; 病原体基因组的地理分布。 Test geological hypotheses; elucidate regional or intercontinental geological processes; history of diversity; addressing uncertainties in geological reconstruction and scale effects; geographic distribution of the genomes of pathogens.	10³-10⁶	区域 Regional	亚马孙河形成; 安第斯山脉隆升历史等。 Drainage basin reconfiguration of Amazon through time; Andean uplift history, etc.	Baker et al, 2014; Dolby et al, 2022

学科 Disciplines	方法和数据 Methods and data	研究问题 Research question	时间尺度 Temporal scale (yr)^*	空间尺度 Spatial scale	应用 Applications	参考文献 References
谱系生物地理学 Phylogeography	方法: 系统发育重建; 谱系结构分析; 中性理论; 最大熵模型; 生态位模型; 谱系多样性; 区系相似性分析; 分子钟分析; 谱系扩散隔离分析等。数据: 分子遗传数据; 气候变化, 环境; 化石; 物种地理分布; 系统发育; 土地利用; 人类活动等。 Methods: Phylogenetic reconstruction; genetic structure analysis; neutral theory; maximum entropy model; ecological niche modeling; phylogenetic diversity; floral similarity analysis; molecular clock analysis; dispersal-vicariance analysis, etc. Data: Genetic data; climate change; environmental; fossil; geographical distribution of species; phylogeny; land use; human activities, etc.	谱系的地理分布和种群的进化历史等。 Geographic distribution of lineages; evolutionary history of populations	10³-10⁶	局部-区域 Local- regional	物种形成假说检验; 物种遗传多样性分析; 物种分化研究; 扩散和隔离分化研究等。 Speciation hypothesis testing; genetic diversity analysis of species; species differentiation; dispersal-vicariance -divergence, etc.	Emerson & Hewitt, 2005; Avise, 2009
景观遗传学 Landscape genetics	方法: Mantel检验; 遗传多样性估计; 结构方程模型; 最小成本路径分析; Monmonier最大差异算法; 回归分析; 距离隔离检验等。数据: 分子遗传; 环境变化; 土地利用; 人类活动等。 Methods: Mantel test; genetic diversity estimates; structural equation models; least cost paths analysis; Monmonier’s maximum difference algorithm; regression analysis; isolation-by-distance test, etc. Data: Genetic data; environmental change; land use; human activities, etc.	景观结构的遗传效应; 景观对基因流动的影响; 基于物种的时空尺度耦合等。 Genetic effects of landscape structure; influence of landscape on gene flow; spatio-temporal scale coupling based on species	10-10²	局部-区域 Local- regional	确定保护单元; 评估种群状况; 管理入侵物种; 种群恢复等。 Identification of conservation units; assessment of population status; management of invasive species; population recovery, etc.	Manel et al, 2003; Segelbacher et al, 2010; 沈泽昊和吉成均, 2010
保护遗传学 Conservation genetics	方法: 遗传多样性分析; 贝叶斯聚类分析; 物种分布模拟等。数据: 分子遗传数据; 物种分布数据等。 Methods: Genetic diversity analysis; Bayesian cluster analysis; species distribution modeling, etc. Data: Genetic data; geographical distribution of species, etc.	濒危物种保护; 遗传多样性保护; 保持物种进化潜力等。 Conservation of endangered species; conservation of genetic diversity; preservation of species’ evolutionary potential, etc.	10-10²	局部- 区域 Local- regional	评估种群结构; 确定物种保护单元; 保护管理对策制定等。 Population structure assessment; identification of species conservation units; formulation of conservation management strategies, etc.	Hedrick, 2001; 谭鑫鑫和李明, 2018
保护生物地理学 Conservation biogeography	方法: 物种丰富度和特有性分析; 遗传多样性估计; 空间多样性分析; GIS; 基因流分析; 敏感性分析; 网络分析; 物种分布模型; 生态位模型; 生物气候包络模型等。数据: 分子遗传; 物种分布数据; 遥感; 土地利用; 人类活动等。 Methods: Species richness and endemic analysis; genetic diversity estimates; spatial diversity analysis; GIS; gene flow; sensitivity analysis; network analysis; species distribution modeling; ecological niche modeling; bioclimate envelope modeling, etc. Data: Genetic data; geographical distribution of species; remote sensing; land use; human activities, etc.	生物多样性保护; 生态格局与过程的时空动态和保护决策等。 Biodiversity conservation; temporal and spatial dynamics of ecological patterns and processes and conservation decisions, etc.	10³-10⁶	区域- 全球 Regional- global	评估种群规模; 保护区规划; 物种分布模拟; 物种入侵模式和驱动因素分析; 自然保护区评估; 气候避难所的识别等。 Assessment of population size; protected area planning; species distribution modeling; species invasion patterns and driving factors analysis; assessment of nature reserve; identification of climate refuges, etc.	Whittaker et al, 2005; Richardson & Whittaker, 2010
生物地理学 Biogeography	方法: 空间自相关分析; 热点分析; Mantel检验; 贝叶斯分析; 遗传结构分析; 系统发育分析; 物种分布模型; 谱系地理格局分析; 物种扩散-灭绝模型; 生态位模型等。数据: 分子遗传; 遥感; 气候变化; 环境; 物种分布; 古气候; 化石; 土地利用; 人类活动等。 Methods: Spatial autocorrelation analysis; hotspot analysis; Mantel test; Bayesian analysis; genetic structure analysis; phylogenetic analysis; species distribution modeling; phylogeographical pattern analysis; dispersal-extinction analysis; ecological niche modeling, etc. Data: Genetic data; remote sensing; climate change; environmental; geographical distribution of species; paleoclimate; fossil; land use; human activities, etc.	现存物种的起源; 物种分布模式; 植物区系; 生物多样性保护等。 Origin of existing species; distribution patterns of species; flora; biodiversity conservation, etc.	10-10⁶	区域- 全球 Regional- global	植物区系划分; 山地植被与地理环境的关系; 物种起源扩散研究等。 Division of flora; the relationship between mountain vegetation and geographic environment; species origin and diffusion, etc.	McDowall, 2004; Wiens & Donoghue, 2004; Posadas et al, 2006
地理基因组学 Geogenomics	方法: 年代学分析; 岩相分析; 地球化学分析; 隔离屏障模拟分析; 系统发育分析; 遗传结构分析、基因流分析; 分化时间分析; 种群动态分析; 情景模拟分析; 一致性检验; 统计假设检验等。数据: 分子遗传; 物种分布数据; 遥感; 地质与历史事件; 地质年代; 沉积学; 古气候等。 Methods: Chronological analysis; petrographic analysis; geochemical analysis; dispersal- vicariance simulation analysis; phylogenetic analysis; genetic structure analysis; gene flow analysis; differentiation time analysis; population dynamics analysis; scenario simulation analysis; concordance test; statistical hypothesis testing, etc. Data: Genetic data; geographical distribution of species; remote sensing; geological and historical events; geologic age; sedimentary evidence; paleoclimate, etc.	检验地质假说; 阐明区域或洲际地质过程; 多样性历史分析; 地质重建中的不确定性与尺度效应; 病原体基因组的地理分布。 Test geological hypotheses; elucidate regional or intercontinental geological processes; history of diversity; addressing uncertainties in geological reconstruction and scale effects; geographic distribution of the genomes of pathogens.	10³-10⁶	区域 Regional	亚马孙河形成; 安第斯山脉隆升历史等。 Drainage basin reconfiguration of Amazon through time; Andean uplift history, etc.	Baker et al, 2014; Dolby et al, 2022

研究区域 Areas	研究类群 Taxa	参考文献 References
亚马孙河 Amazon River	哺乳动物(灵长类动物); 鸟类; 植物(灌木、乔木); 爬行动物 Mammal (primates); bird; plants (shrubs; trees); reptiles	Pupim et al, 2019; Ribas et al, 2022; Luna et al, 2023; Musher et al, 2024
安第斯山脉 Andean Mountains	植物(乔木); 节肢动物(昆虫) Plants (trees); arthropods (insects)	Gianni et al, 2020; Murienne et al, 2022; Sanín et al, 2022; Fasanella et al, 2023
太平洋岛屿 Pacific Islands	节肢动物(蜘蛛) Arthropods (spiders)	Elias et al, 2024
日本 Japan	鱼类 Fish	Masuda et al, 2023
全球 Global	二倍体真核生物(哺乳动物; 爬行动物; 鱼类; 鸟类; 无脊椎动物; 植物(非乔木; 乔木)) Diploid eukaryotes (mammal; reptiles; fish; bird; invertebrate; plants (non-tree; trees))	Araya-Donoso et al, 2022
阿尔卑斯山 Alps	哺乳动物(臆羚) Mammal (northern chamois)	Leugger et al, 2022
青藏高原 Qinghai-Tibetan Plateau	植物(乔木; 灌木; 草本); 两栖动物; 爬行动物; 节肢动物(蜘蛛); 鱼类; 鸟类 Plants (trees; shrubs; herbs); amphibians; reptiles; arthropods (spiders); fish; birds	Song et al, 2021; Xu et al, 2021; Luo & Li, 2022; Yang et al, 2023; 李茜茜等, 2023
全球 Global	病原体 Pathogens	Sargeant et al, 2014; Tarr et al, 2018; Tang et al, 2022a, b, 2023; Jiang et al, 2023