Ten Years of Landscape Genomics: Challenges and Opportunities

Landscape genomics is a relatively new discipline that aims to reveal the relationship between adaptive genetic imprints in genomes and environmental heterogeneity among natural populations. Although the interest in landscape genomics has increased since this term was coined, studies on this topic remain scarce. Landscape genomics has become a powerful method to scan and determine the genes responsible for the complex adaptive evolution of species at population (mostly) and individual (more rarely) level. This review outlines the sampling strategies, molecular marker types and research categories in 37 articles published during the first 10 years of this field (i.e., 2007–2016). We also address major challenges and future directions for landscape genomics. This review aims to promote interest in conducting additional studies in landscape genomics.

• Publication year

  2017

• Venue

  Frontiers in Plant Science

• Publication date

  2017-12-12

• Fields of study

  Biology, Geography, Medicine, Environmental Science

• Identifiers
  DOI 10.3389/fpls.2017.02136PMID 29312391PMCID 5733015
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Numerical Ecology

  2019influential reference
• Development of Chloroplast and Nuclear DNA Markers for Chinese Oaks (Quercus Subgenus Quercus) and Assessment of Their Utility as DNA Barcodes

  2017cited by this paper
• Landscape genomics reveal that ecological character determines adaptation: a case study in smoke tree (Cotinus coggygria Scop.)

  2017cited by this paper
• Landscape Population Genomics of Forsythia (Forsythia suspensa) Reveal That Ecological Habitats Determine the Adaptive Evolution of Species

  2017influential reference
• Environmental versus geographical effects on genomic variation in wild soybean (Glycine soja) across its native range in northeast Asia

  2016cited by this paper
• TESS3: fast inference of spatial population structure and genome scans for selection

  2016cited by this paper
• Climate-related adaptive genetic variation and population structure in natural stands of Norway spruce in the South-Eastern Alps

  2016cited by this paper
• Contributions of historical and contemporary geographic and environmental factors to phylogeographic structure in a Tertiary relict species, Emmenopterys henryi (Rubiaceae)

  2016cited by this paper
• Signatures of natural selection on Pinus cembra and P. mugo along elevational gradients in the Alps

  2016cited by this paper
• Evidence of divergent selection for drought and cold tolerance at landscape and local scales in Abies alba Mill. in the French Mediterranean Alps

  2016cited by this paper
• Riverscape genomics of a threatened fish across a hydroclimatically heterogeneous river basin

  2016cited by this paper
• Patterns of neutral and adaptive genetic diversity across the natural range of sugar pine (Pinus lambertiana Dougl.)

  2016cited by this paper
• Genome-environment association study suggests local adaptation to climate at the regional scale in Fagus sylvatica.

  2016cited by this paper
• Local adaptation to temperature and precipitation in naturally fragmented populations of Cephalotaxus oliveri, an endangered conifer endemic to China

  2016cited by this paper
• Environmental adaptation in Chinook salmon (Oncorhynchus tshawytscha) throughout their North American range

  2015influential reference
• A practical guide to environmental association analysis in landscape genomics

  2015influential reference
• Isolation by distance, resistance and/or clusters? Lessons learned from a forest‐dwelling carnivore inhabiting a heterogeneous landscape

  2015cited by this paper
• Adaptation to Low Salinity Promotes Genomic Divergence in Atlantic Cod (Gadus morhua L.)

  2015cited by this paper
• Isolation by environment in White‐breasted Nuthatches (Sitta carolinensis) of the Madrean Archipelago sky islands: a landscape genomics approach

  2015cited by this paper
• Landscape genomics and a common garden trial reveal adaptive differentiation to temperature across Europe in the tree species Alnus glutinosa

  2014cited by this paper
• Isolation by environment

  2014cited by this paper
• A first look at the Oxford Nanopore MinION sequencer

  2014cited by this paper
• Genomic Signature of Adaptation to Climate in Medicago truncatula

  2014cited by this paper
• EXAMINING THE FULL EFFECTS OF LANDSCAPE HETEROGENEITY ON SPATIAL GENETIC VARIATION: A MULTIPLE MATRIX REGRESSION APPROACH FOR QUANTIFYING GEOGRAPHIC AND ECOLOGICAL ISOLATION

  2013cited by this paper
• DISENTANGLING THE EFFECTS OF GEOGRAPHIC AND ECOLOGICAL ISOLATION ON GENETIC DIFFERENTIATION

  2013influential reference
• Putting the landscape into the genomics of trees: approaches for understanding local adaptation and population responses to changing climate

  2013cited by this paper
• INTEGRATING LANDSCAPE GENOMICS AND SPATIALLY EXPLICIT APPROACHES TO DETECT LOCI UNDER SELECTION IN CLINAL POPULATIONS

  2013cited by this paper
• The magnitude of local adaptation under genotype-dependent dispersal

  2013cited by this paper
• The role of selection in driving landscape genomic structure of the waterflea Daphnia magna

  2013cited by this paper
• Detecting selection along environmental gradients: analysis of eight methods and their effectiveness for outbreeding and selfing populations

  2013cited by this paper
• A High-Density Gene Map of Loblolly Pine (Pinus taeda L.) Based on Exome Sequence Capture Genotyping

  2013cited by this paper
• Ten years of landscape genetics.

  2013cited by this paper
• LANDSCAPE GENOMICS IN ATLANTIC SALMON (SALMO SALAR): SEARCHING FOR GENE–ENVIRONMENT INTERACTIONS DRIVING LOCAL ADAPTATION

  2013cited by this paper
• Quantifying the roles of ecology and geography in spatial genetic divergence.

  2013cited by this paper
• SLAF-seq: An Efficient Method of Large-Scale De Novo SNP Discovery and Genotyping Using High-Throughput Sequencing

  2013cited by this paper
• Testing for Associations between Loci and Environmental Gradients Using Latent Factor Mixed Models

  2012influential reference
• Sampling for Microsatellite-Based Population Genetic Studies: 25 to 30 Individuals per Population Is Enough to Accurately Estimate Allele Frequencies

  2012cited by this paper
• Robust Identification of Local Adaptation from Allele Frequencies

  2012cited by this paper
• A model-based approach for analysis of spatial structure in genetic data

  2012influential reference
• Sampling in landscape genomics.

  2012cited by this paper
• Differential effects of landscape‐level environmental features on genetic structure in three codistributed tree species in Central America

  2012cited by this paper
• A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species

  2011cited by this paper
• Dismantling the Mantel tests

  2011cited by this paper
• Climate change and evolutionary adaptation

  2011cited by this paper
• Detecting Selection in Population Trees: The Lewontin and Krakauer Test Extended

  2010cited by this paper
• Using Environmental Correlations to Identify Loci Underlying Local Adaptation

  2010cited by this paper
• Genetic structure is correlated with phenotypic divergence rather than geographic isolation in the highly polymorphic strawberry poison‐dart frog

  2010cited by this paper
• Statistical approaches in landscape genetics: an evaluation of methods for linking landscape and genetic data

  2009cited by this paper
• Detecting loci under selection in a hierarchically structured population

  2009cited by this paper
• Perspectives of DNA microarray and next-generation DNA sequencing technologies

  2009cited by this paper
• High-throughput genotyping and mapping of single nucleotide polymorphisms in loblolly pine (Pinus taeda L.)

  2008cited by this paper
• Efficient Control of Population Structure in Model Organism Association Mapping

  2008cited by this paper
• Genome-wide association to fine-scale ecological heterogeneity within a continuous population of Biscutella laevigata (Brassicaceae).

  2008cited by this paper
• Adaptation, migration or extirpation: climate change outcomes for tree populations

  2008cited by this paper
• Landscape genetics and hierarchical genetic structure in Atlantic salmon: the interaction of gene flow and local adaptation

  2008cited by this paper
• A Genome-Scan Method to Identify Selected Loci Appropriate for Both Dominant and Codominant Markers: A Bayesian Perspective

  2008cited by this paper
• The Structure of Clines with Fitness‐Dependent Dispersal

  2008cited by this paper
• Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers.

  2007influential reference
• TASSEL: software for association mapping of complex traits in diverse samples

  2007influential reference
• A spatial analysis method (SAM) to detect candidate loci for selection: towards a landscape genomics approach to adaptation

  2007influential reference
• Analyzing spatial autocorrelation in species distributions using Gaussian and logit models

  2007cited by this paper
• ISOLATION BY RESISTANCE

  2006cited by this paper
• Conceptual issues in local adaptation

  2004cited by this paper
• The consequences of spatial structure for the design and analysis of ecological field surveys

  2002cited by this paper
• Canoco reference manual and CanoDraw for Windows user''s guide: software for canonical community ord

  2002cited by this paper
• Spatial Autocorrelation: Trouble or New Paradigm?

  1993cited by this paper
• ISOLATION BY DISTANCE IN EQUILIBRIUM AND NON‐EQUILIBRIUM POPULATIONS

  1993cited by this paper
• Distribution of gene frequency as a test of the theory of the selective neutrality of polymorphisms.

  1973cited by this paper
• The detection of disease clustering and a generalized regression approach.

  1967cited by this paper

• Leveraging Knowledge of Traditional Italian Maize Landrace Diversity to Identify Signals of Local Adaptation

  2026cites this paper
• Computational analysis and modeling of climate impact on Pteridium aquilinum (L.) populations

  2025cites this paper
• Lithobiomes Heterogeneity and Geographic Distance Shape the Landscape Genomics Within Brazilian Mountain Systems

  2025cites this paper
• Genetic structure and local adaptation of Nitraria sphaerocarpa populations from arid northwestern China

  2025cites this paper
• Gene-ecological studies of critically isolated fern Pteris dentata Forssk.: genetic diversity, environmental adaptation, and future distribution modeling (SDM)

  2025cites this paper
• Genomic Insights into the Origin, High Fecundity and Environmental Adaptation of Hu Sheep

  2025cites this paper
• Genomic Exploration of Climate-driven Evolution and Evolutionary Convergence in Forest Pathogens

  2025cites this paper
• Potential regulation of cleistogamy in pigeonpea through jasmonic acid and bHLH transcription factor interactions

  2025cites this paper
• Monitoring and Modeling the Soil‐Plant System Toward Understanding Soil Health

  2025influential citation
• Negotiating a Fragmented World: What Do We Know, How Do We Know It, and Where Do We Go from Here?

  2025cites this paper
• Linking landscape and genetic variation in the heterogeneous Yungas Andean forest' hotspot: a multi taxa approach

  2024cites this paper
• Optimising Sampling Design for Landscape Genomics

  2024cites this paper
• South African indigenous chickens' genetic diversity, and the adoption of ecological niche modelling and landscape genomics as strategic conservation techniques

  2024cites this paper
• Demographic History and Adaptive Evolution of Indo‐Pacific Bottlenose Dolphins (Tursiops aduncus) in Western Australia

  2024cites this paper
• A new computational method to estimate adaptation time in Avicennia by using divergence time

  2024cites this paper
• Comparative landscape genomics reveals species-specific spatial patterns and suggests human-aided dispersal in a global hotspot for biological invasions

  2024cites this paper
• Climatic fluctuations, geographic features, and evolutionary forces: Shaping high genomic diversity and local adaptation in Muntiacus reevesi

  2024cites this paper
• Conserving Evolutionary Potential: Combining Landscape Genomics with Established Methods to Inform Plant Conservation.

  2024cites this paper
• Landscape genomics reveals regions associated with adaptive phenotypic and genetic variation in Ethiopian indigenous chickens

  2024cites this paper
• The geno-geo-climate nexus: contributions of geographic and ecological factors in shaping the genomic divergence of two closely related threatened rainforest species of Fontainea Heckel (Euphorbiaceae)

  2024cites this paper
• Rolling with the punches: Organism-environment interactions shape spatial pattern of adaptive differentiation in the widespread mantis shrimp Oratosquilla oratoria.

  2024cites this paper
• Genetic divergence and ecological adaptation of an eastern North American spring ephemeral Sanguinaria canadensis

  2024cites this paper
• Whole genome analyses reveal weak signatures of population structure and environmentally associated local adaptation in an important North American pollinator, the bumble bee Bombus vosnesenskii

  2023cites this paper
• Landscape genomics reveals adaptive genetic differentiation driven by multiple environmental variables in naked barley on the Qinghai-Tibetan Plateau

  2023cites this paper
• Genomic signals of local adaptation in Picea crassifolia

  2023cites this paper
• Using Landscape Genomics to Assess Local Adaptation of Fruit trees to Current and Future Climatic Conditions

  2023cites this paper
• Landscape genomics reveals adaptive divergence of indigenous sheep in different ecological environments of Xinjiang, China.

  2023cites this paper
• Space‐for‐time substitutions in climate change ecology and evolution

  2023cites this paper
• Approach and prospects of landscape genetics in livestock: A review

  2023cites this paper
• Adaptive divergence and genetic vulnerability of relict species under climate change: a case study of Pterocarya macroptera

  2023cites this paper
• Neutral and adaptive genetic diversity in plants: An overview

  2023cites this paper
• Genomic insights into genetic diversity and local adaptation of a dominant desert steppe feather grass, Stipa breviflora Griseb.

  2023cites this paper
• Putative Local Adaptive SNPs in the Genus Avicennia

  2023cites this paper
• Environmental selection, rather than neutral processes, best explain regional patterns of diversity in a tropical rainforest fish

  2023cites this paper
• Is the São Francisco River a historical barrier to gene flow for populations of Melipona mandacaia Smith, 1863 (Hymenoptera: Apidae)?

  2023cites this paper
• Comparative analysis of cold-responsive genes under short-term cold stimulation and cold-adaptive genes under long-term heterogeneous environments reveals a cold adaptation mechanism in weeping forsythia

  2022cites this paper
• Predicting climate change-related genetic offset for the endangered southern South American conifer Araucaria araucana

  2022cites this paper
• Adaptive potential of Coffea canephora from Uganda in response to climate change

  2022influential citation
• EST-SSR Primer Development and Genetic Structure Analysis of Psathyrostachys juncea Nevski

  2022cites this paper
• The Biological Hierarchy, Time, and Temporal 'Omics in Evolutionary Biology: A Perspective.

  2022cites this paper
• Urban-rural gradients: how landscape changes drive adaptive evolution of plant competitive traits

  2022cites this paper
• Using landscape genomics to delineate future adaptive potential for climate change in the Yosemite toad (Anaxyrus canorus)

  2022cites this paper
• Impacts of Land Use Change on Landscape Structure and Ecosystem Services at Local Scale: A Case Study in Central Portugal

  2022cites this paper
• Impacts of Land Use Change on Landscape Structure and Ecosystem Services at Local Scale: A Case Study in Central Portugal

  2022cites this paper
• Genetic Adaptation of Livestock to Heat Stress Challenges

  2021cites this paper
• Large-scale genome-wide study reveals climate adaptive variability in a cosmopolitan pest

  2021cites this paper
• Landscape genomics of the streamside salamander: Implications for species management in the face of environmental change

  2021cites this paper
• Genetic divergence and local adaptation of Liriodendron driven by heterogeneous environments

  2021cites this paper
• Quercus Conservation Genetics and Genomics: Past, Present, and Future

  2021cites this paper
• Non-linear genetic diversity and notable population differentiation caused by low gene flow of bermudagrass [Cynodon dactylon (L.) Pers.] along longitude gradients

  2021cites this paper
• Next-Generation Sequencing and Its Impacts on Entomological Research in Ecology and Evolution

  2021cites this paper
• Reefscape Genomics: Leveraging Advances in 3D Imaging to Assess Fine-Scale Patterns of Genomic Variation on Coral Reefs

  2021cites this paper
• Optimizing sampling design and sequencing strategy for the genomic analysis of quantitative traits in natural populations

  2021cites this paper
• Demographic history and local adaptation of Myripnois dioica (Asteraceae) provide insight on plant evolution in northern China flora

  2021cites this paper
• Transcriptomic responses to drought stress among natural populations provide insights into local adaptation of weeping forsythia

  2021cites this paper
• Prospects for Trifolium Improvement Through Germplasm Characterisation and Pre-breeding in New Zealand and Beyond

  2021cites this paper
• Geographical and environmental contributions to genomic divergence in mangrove forests

  2021cites this paper
• The evolutionary dynamics of biological invasions: A multi‐approach perspective

  2021cites this paper
• Primate landscape genetics: A review and practical guide

  2021cites this paper
• Comparative analysis of drought-responsive and -adaptive genes in Chinese wingnut (Pterocarya stenoptera C. DC)

  2021cites this paper
• Landscape Genetics: From Classic Molecular Markers to Genomics

  2020cites this paper
• Genetic variability and structure of an important wild steppe grass Psathyrostachys juncea (Triticeae: Poaceae) germplasm collection from north and central Asia

  2020cites this paper
• Geographic and environmental contributions to genomic divergence in mangrove forests

  2020cites this paper
• Evolutionary genomics can improve prediction of species’ responses to climate change

  2020cites this paper
• Population Transcriptomes Reveal the Interspecific Adaptive Genetic Differentiation of Liriodendron by Landscape Genetics

  2020cites this paper
• Landscape genomics reveals genetic evidence of local adaptation in a widespread tree, the Chinese wingnut (Pterocarya stenoptera)

  2020cites this paper
• Landscape Genomics of a Widely Distributed Snake, Dolichophis caspius (Gmelin, 1789) across Eastern Europe and Western Asia

  2020cites this paper
• Plant adaptation to climate change—Where are we?

  2020cites this paper
• Genome sequencing and population genomics modeling provide insights into the local adaptation of weeping forsythia

  2020cites this paper
• Influence of isolation by environment and landscape heterogeneity on genetic structure of wild rice Zizania latifolia along a latitudinal gradient

  2020cites this paper
• Evaluating genomic data for management of local adaptation in a changing climate: A lodgepole pine case study

  2019cites this paper
• Adaptive Introgression Promotes Fast Adaptation In Oaks Marginal Populations

  2019cites this paper
• Landscape genetics reveals that adaptive genetic divergence in Pinus bungeana (Pinaceae) is driven by environmental variables relating to ecological habitats

  2019cites this paper
• Hybridization between two parapatric ranid frog species in the northern Sierra Nevada, California, USA

  2019cites this paper
• Environmental factors impacting Saprolegnia infections in wild fish stocks

  2019cites this paper
• Molecular Phylogeography Analysis Reveals Population Dynamics and Genetic Divergence of a Widespread Tree Pterocarya stenoptera in China

  2019cites this paper
• Borrelia bavariensis: Vector Switch, Niche Invasion, and Geographical Spread of a Tick-Borne Bacterial Parasite

  2019cites this paper
• Improving Standards for At-Risk Butterfly Translocations

  2018cites this paper
• Adaptive genetic differentiation in Pterocarya stenoptera (Juglandaceae) driven by multiple environmental variables were revealed by landscape genomics

  2018cites this paper
• Deciphering the drivers of negative species–genetic diversity correlation in Alpine amphibians

  2018cites this paper
• Eco-Evolutionary Dynamics: The Predator-Prey Adaptive Play and the Ecological Theater

  2018cites this paper
• Edinburgh Research Explorer Space-for-time substitutions in climate change ecology and evolution

  year unknowncites this paper