The Genomic Kaleidoscope: On the Hidden Dimensions of Within-Species Genomic Diversity

Genomic diversity within species encompasses a range of sequence-related, structural, and regulatory features. To illustrate their complexity, we invoke the analogy of a kaleidoscope: while the DNA sequence represents its core, the genome has a dynamic, multidimensional configuration shaped by interactions across these features, generating an array of dimensions of genomic variation. In this perspective, we highlight underexplored dimensions of genomic variation that contribute to phenotypic diversity. We begin by revisiting the existence of noncanonical chromosomes and by emphasizing the role of large-scale structural changes and the 3D genome architecture in modulating genomic function. We then examine the regulatory mechanisms shaping transcriptional activity and genetic variation that, instead of regulating mean trait values, defines the degree of trait variability. Finally, we discuss the influence of sequence composition on its mutational potential. These dimensions, though rooted in sequence, are context dependent, interconnected, and often difficult to disentangle, reflecting a level of structural and regulatory complexity that challenges traditional genotype-phenotype models. By synthesizing recent findings across these dimensions, we argue for a broader framework for studying within-species genomic diversity: one that accounts for the diverse molecular architectures underlying phenotypic output. This expanded view not only deepens our knowledge of the genome itself but also contributes to our understanding of genome evolution and within-species phenotypic variation.

Authors

Institutions

Publication Details

Journal
Genome Biology and Evolution
Published
2025-10-29
DOI
https://doi.org/10.1093/gbe/evaf204
Citations
1
Primary Topic
Genetic diversity and population structure
Type
article
Field-Weighted Citation Impact
1.82

Funders

Controls
|||
ALL TIME
JAN
FEB
MAR
APR
MAY
JUN
JUL
AUG
SEP
OCT
article

The Genomic Kaleidoscope: On the Hidden Dimensions of Within-Species Genomic Diversity

Justin J. S. Wilcox, Diego A. Hartasánchez, Gabriela Santos‐Rodriguez, Aurora Ruiz‐Herrera et al.
1 citations
Genome Biology and Evolution
Genetic diversity and population structure
1.82
article

The Genomic Kaleidoscope: On the Hidden Dimensions of Within-Species Genomic Diversity

Justin J. S. Wilcox, Diego A. Hartasánchez, Gabriela Santos‐Rodriguez, Aurora Ruiz‐Herrera, Thea F. Rogers, Luisa F. Pallares, Mayra Furlan-Magaril, Marina Brasó‐Vives, Christabel Floi Bucao, Julien F. Ayroles, Paco Majic, Nikolas Vellnow, Juan Antonio Rodríguez, James Phipps-Tan
article en
1 citations

Abstract

Genomic diversity within species encompasses a range of sequence-related, structural, and regulatory features. To illustrate their complexity, we invoke the analogy of a kaleidoscope: while the DNA sequence represents its core, the genome has a dynamic, multidimensional configuration shaped by interactions across these features, generating an array of dimensions of genomic variation. In this perspective, we highlight underexplored dimensions of genomic variation that contribute to phenotypic diversity. We begin by revisiting the existence of noncanonical chromosomes and by emphasizing the role of large-scale structural changes and the 3D genome architecture in modulating genomic function. We then examine the regulatory mechanisms shaping transcriptional activity and genetic variation that, instead of regulating mean trait values, defines the degree of trait variability. Finally, we discuss the influence of sequence composition on its mutational potential. These dimensions, though rooted in sequence, are context dependent, interconnected, and often difficult to disentangle, reflecting a level of structural and regulatory complexity that challenges traditional genotype-phenotype models. By synthesizing recent findings across these dimensions, we argue for a broader framework for studying within-species genomic diversity: one that accounts for the diverse molecular architectures underlying phenotypic output. This expanded view not only deepens our knowledge of the genome itself but also contributes to our understanding of genome evolution and within-species phenotypic variation.

Genome Biology and EvolutionVol. 17(11)
Universitat Autònoma de Barcelona (ES), University of Copenhagen (DK), SIB Swiss Institute of Bioinformatics (CH), The University of Sydney (AU), University of Vienna (AT), TU Dortmund University (DE), Princeton University (US), UNSW Sydney (AU), New South Wales Institute of Psychiatry (AU), European Molecular Biology Laboratory (DE), Friedrich Miescher Laboratory (DE), European Molecular Biology Laboratory (DE), Universidad Nacional Autónoma de México (MX), University of Lausanne (CH)
National Science Foundation, International Max Planck Research School for Environmental, Cellular and Molecular Microbiology, Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung, Institució Catalana de Recerca i Estudis Avançats, Max-Planck-Gesellschaft, Novo Nordisk, Ministerio de Ciencia e Innovación, Novo Nordisk Fonden, Ministerio de Asuntos Económicos y Transformación Digital, Gobierno de España, Agència de Gestió d'Ajuts Universitaris i de Recerca, Agencia Estatal de Investigación
Openalex Percentile: Top 11%
Genetic diversity and population structure
1.82
DOIOpen Access PDFOpenAlex
AI Navigator

Ask Laika to Summarize, Analyze, and Connect papers live on the map.

Summarize Papers & Methodologies

Extract key findings, datasets, and comparative methods across publications.

Benchmark Rankings & Visual Analytics

Rank top research institutions, authors, funders, topics, and journals by Field-Weighted Citation Impact (FWCI) and paper volume with instant charts.

Connect Distant Disciplines

Bridge topological clusters on the map to find hidden collaborative intersections.