In the complex tapestry of plant evolution, polyploidy – the presence of more than two sets of chromosomes – often acts as a pivotal mechanism driving diversification and adaptation. A recent groundbreaking study has shed light on one such polyploid wild relative of barley, Hordeum bulbosum, which intriguingly contains both diploid and tetraploid individuals that, despite their distinct genomic configurations, exhibit near-identical morphologies. This conundrum has puzzled botanists and geneticists alike: how do these cytotypes arise, how are they related, and is there ongoing genetic exchange between them? The latest research employs cutting-edge genomic analyses, mapping 32 diverse haplotypes alongside 263 lineages, to unlock the evolutionary history and genetic intricacies of these plants, revealing a compelling story of multiple tetraploid origins and intricate population dynamics.

The investigation began by sequencing and genotyping a broad spectrum of H. bulbosum individuals, combining nuclear and chloroplast gene data to construct detailed phylogenetic trees. These trees uncovered four ancestral populations, each with unique genetic signatures that transcended the simplistic view of diploid and tetraploid division. Despite clear differentiation in chromosome numbers and genome sizes, the morphological similarity between the cytotypes begged the question of their evolutionary timeline and interactions. By pairing these genetic insights with geographic distribution data, the study paints a nuanced picture of H. bulbosum’s evolutionary past, weaving in the geological and climatic events that shaped their divergence.

One of the most intriguing revelations comes from a diploid accession from Libya, designated PI365428, representing an ancient and divergent lineage. This population appears to have split from other H. bulbosum genotypes around 2 million years ago, possibly making it a relic of early diploid populations in the eastern Mediterranean or North Africa. The researchers linked its recent population decline to environmental shifts, notably the Sahara’s desertification starting about 10,000 years ago. This finding underscores how climatic upheavals influence genetic variation and population structure, and also highlights the enduring legacy of ancient lineages hidden within modern plant populations.

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In stark contrast, certain more geographically localized lineages, such as FB19-001-1 from the Peloponnese region of Greece, displayed remarkably recent divergence patterns. Population size trajectories for FB19-001-1 closely mirrored those of nearby diploid populations, suggesting a more recent emergence of this tetraploid lineage. Conversely, a tetraploid individual from Tajikistan, GRA2256-1, separated from Greek diploids approximately 1.5 million years ago, representing an older, more genetically isolated polyploid lineage. This disparity in divergence times implies a complex polyploid landscape shaped by multiple independent tetraploidization events rather than a single origin.

The geographic distribution of these lineages further amplifies this narrative. Genetic clustering places Greek tetraploids in closest affinity with local diploid populations rather than distant tetraploids, with their transposable element profiles—a vital genomic signature—mirroring those of nearby diploids. This genetic proximity suggests localized tetraploid origins and ongoing gene flow between cytotypes in certain regions. Indeed, Greece emerges as a genetic melting pot where hybridization between older and younger tetraploid lineages occurs, particularly across the Peloponnese and western mainland. These patterns are underscored by admixture analyses that reveal distinct ancestry proportions corresponding to divergent lineage contributions.

Perhaps most fascinating is the evidence for multiple independent polyploidization events within H. bulbosum. Population genetic analyses reveal that the SNP-based divergence between older tetraploid lineages corresponds to splits dating back over 2 million years, confirming that polyploidy arose multiple times in this taxon’s evolutionary history. Shared ancestral haplotype groups (AHGs), identified through sophisticated computational tools like IntroBlocker, align neatly with these population distinctions, providing a fine-scaled view of genetic contributions and inter-lineage hybridization. For instance, admixed tetraploid FB19-028-3 carries significant genomic fractions derived from both older polyploid groups and western Mediterranean diploids, illustrating the mosaic nature of these genomes.

The study also addresses reproductive isolation and gene flow between diploids and tetraploids—a dynamic essential to understanding the evolutionary viability of polyploids. Even though cytotypes are separated by chromosome count and genetic background, their morphological indistinguishability challenges assumptions about reproductive barriers. In Greece, the Pindos mountain range forms a geographic barrier that delineates diploid from tetraploid distributions, yet hybrid zones persist where these ranges overlap. These zones likely represent sites of ongoing admixture and genetic exchange, indicating that polyploidization events have been frequent and evolutionarily recent enough to leave detectable genetic signatures.

From a methodological standpoint, the authors employed a multi-pronged approach, integrating neighbor-joining phylogenies with model-based ancestry estimation using ADMIXTURE, pairwise sequentially Markovian coalescent (PSMC) analyses to reconstruct population size histories, and haplotype-based tools to detect shared genomic blocks across lineages. This comprehensive toolkit allowed a robust inference of divergence times, hybridization events, and the complexity of population structure, emphasizing the power of current genomic technologies in unraveling polyploid origins.

These findings not only refine our understanding of Hordeum bulbosum but also broadly inform evolutionary biology concepts surrounding speciation, genome duplication, and adaptive radiation. The multiple independent origins of polyploidy within a single species complex challenge classical views of a singular polyploid ancestor and suggest ongoing, dynamic processes of genomic restructuring and hybridization. Moreover, the persistence of morphological similarity despite deep genomic differences highlights intriguing aspects of phenotypic evolution and plasticity, important considerations for crop wild relatives and their potential utilization.

Ecologically, H. bulbosum’s story captures the interplay of geological history, climatic pressures, and geographic barriers in shaping plant genomics. The post-glacial desertification of the Sahara, mountain ranges like Pindos, and localized refugia all factor into patterns of divergence, admixture, and polyploid origins. As climate change accelerates, understanding such dynamics becomes crucial for predicting species responses and potential for adaptation in changing environments.

The polyploid pathways unraveled in this work also have practical implications for barley breeding and crop improvement. As a wild relative of barley, H. bulbosum harbors genetic diversity valuable for traits such as disease resistance and environmental tolerance. Clarifying the genomic architecture and evolutionary history of its cytotypes paves the way for targeted introgression and breeding strategies that harness this diversity while navigating challenges posed by chromosomal incompatibilities.

In closing, this expansive genomic investigation into Hordeum bulbosum showcases how modern genomics can decode the enigmatic histories of polyploid species. It reveals that tetraploid cytotypes are not monolithic relics of a single event but are instead the product of multiple evolutionary origins interwoven through admixture and local adaptation. This work thus redefines our understanding of polyploid evolution and charts new avenues for exploring the genomic complexity underlying plant biodiversity.

Subject of Research: Polyploid origins, genomic diversity, and population structure of Hordeum bulbosum, a wild relative of barley.

Article Title: A haplotype-resolved pangenome of the barley wild relative Hordeum bulbosum

Article References:
Feng, JW., Pidon, H., Cuacos, M. et al. A haplotype-resolved pangenome of the barley wild relative Hordeum bulbosum. Nature (2025). https://doi.org/10.1038/s41586-025-09270-x

Tags: Ancestral populations of barleyBarley wild relative geneticsDiploid and tetraploid relationshipsEvolutionary history of barley relativesGenetic exchange in wild relativesGenomic analysis of plant diversityHaplotype-resolved pangenomeHordeum bulbosum studyMorphological similarity in cytotypesPhylogenetic trees in botanyPolyploidy in plant evolutionPopulation dynamics in polyploid plants