🧬 genetics

Range wide analysis of genetic diversity and structure gives insights into Rosa gallica L. evolutionary history

This study utilizes range-wide microsatellite genotyping of 1,618 individuals to reveal that the current distribution of *Rosa gallica* was primarily shaped by post-glacial recolonization from a southern refugium, while also demonstrating a significant contribution of human-mediated dispersal, particularly in France where wild and cultivated lineages frequently overlap.

Original authors: Pawula, C., Clotault, J., Lepais, O., Chastellier, A., Ordonez Trejo, E. J., Thouroude, T., Assini, S., Bakay, L., Bartha, L., Bavcon, J., Cambecedes, J., Cordier, J., Cwener, A., Dajdok, Z., Drevojan

Published 2026-08-11

📖 6 min read🧠 Deep dive

CC BY 4.0

Original authors: Pawula, C., Clotault, J., Lepais, O., Chastellier, A., Ordonez Trejo, E. J., Thouroude, T., Assini, S., Bakay, L., Bartha, L., Bavcon, J., Cambecedes, J., Cordier, J., Cwener, A., Dajdok, Z., Drevojan, P., Garcia, J., Grahic, J., Kapler, A., Kerenyi-Nagy, V., Konjic, A., Łazarski, G., Leblond, N., Mrkvicka, A., Nepras, K., Oliiar, H., Pascale, M., Pejic, I., Piwowarczyk, R., Ravnjak, B., Salvesen, P. H., Sarateanu, V., Schanzer, I., Soldano, A., Tofan-Dorofeev, E., Tomljenovic, N., Wisniewska, K., Wolanin, M., Malecot, V., Grapin, A., Pernet, A.

Original paper licensed under CC BY 4.0 (https://creativecommons.org/licenses/by/4.0/). ⚕️ This is an AI-generated explanation of a preprint that has not been peer-reviewed. It is not medical advice. Do not make health decisions based on this content. Read full disclaimer

Imagine you are a detective trying to solve a mystery that spans thousands of years and half a continent. The suspect? A beautiful, prickly plant called the French Rose (Rosa gallica). To crack the case, scientists use a tool called population genetics. Think of this like a massive DNA fingerprinting party. Just as every person has a unique set of fingerprints, every plant has a unique genetic code. By comparing these codes across different locations, scientists can see who is related to whom, how far they have traveled, and whether they are part of a big family tree or a small, isolated group.

But roses are tricky. They are "polyploids," which is a fancy way of saying they have extra sets of chromosomes, making their genetic code a bit like a complex puzzle with extra pieces. They also reproduce in two ways: by making seeds (like most plants) and by sending out underground runners called "suckers" to clone themselves. This means a single patch of roses might actually be just one giant, spreading clone rather than many different individuals. Furthermore, humans have loved roses for thousands of years, breeding them, swapping them, and planting them in gardens. This makes the mystery even harder: are the roses we see in the wild today there because nature moved them, or because a human gardener planted them centuries ago? Understanding this helps us learn how nature and human history have shaped the world around us.

The Great Rose Mystery: Nature's Journey vs. Human's Garden

In this study, a team of researchers decided to play detective with the French Rose. They wanted to figure out the evolutionary history of this flower: Did it spread across Europe naturally after the last Ice Age, or did humans carry it there? To solve this, they gathered a massive collection of rose samples—1,618 individuals in total! They picked wild roses from 219 different spots across 15 countries, plus some garden varieties and other rose species to compare against.

The scientists used a high-tech method called "SSRseq" to read the DNA of these roses. It's like reading the specific letters in a genetic book to see how similar or different the plants are. Because roses can clone themselves, the team had to be careful. They used a special computer filter to find "clonal lineages"—groups of plants that are genetic twins. If they found a wild rose that was a perfect genetic match to a famous garden rose, they knew a human had likely moved it.

The Big Discovery: Two Different Stories

The results told two very different stories depending on where you looked on the map.

1. The Natural Wanderers (East and South)
In the South Alps (Northern Italy, Slovenia, Croatia) and Central Eastern Europe (places like Poland, Hungary, and Romania), the roses looked like they had a very natural history. The genetic diversity was high, and the patterns suggested that after the last Ice Age, these roses naturally expanded northward from a single "safe haven" (a glacial refugium) in the south. It's like a wave of plants slowly marching up the map as the ice melted, filling the empty spaces with their seeds. The paper suggests this was a natural process, not a human one.

2. The Human-Mediated Travelers (West and France)
The story changes dramatically when you look at France, especially the western and central parts. Here, the genetic structure is much more complex and "structured." The researchers found that the roses in Western France are genetically distinct from those in the East. They have lower genetic diversity, which often happens when a small group of founders starts a new population (a "bottleneck").

Crucially, the study found strong evidence that humans played a huge role here. The team discovered 28 specific sites in France where wild roses were genetic clones of cultivated garden roses. In some cases, a wild rose in a forest was a perfect genetic match to a famous old garden variety like 'Bouquet de Vénus' or 'Rosiers des parfumeurs'. This is the smoking gun: it proves that these wild plants didn't just wander there; they were likely planted by humans, escaped the garden, and took over the wild.

What the Paper Rules Out

The researchers were very careful to test old theories.

They ruled out the idea that the entire European range was colonized by humans during Roman times or the Middle Ages. If humans had carried the roses across the whole continent back then, the genetic patterns would look very different (more uniform and less diverse in the East). The data shows that the Eastern and Southern populations are too diverse and naturally structured to be just human clones.
They ruled out the idea that the Western French populations came from a hidden, ancient "Iberian refuge" (a safe spot in Spain or Portugal during the Ice Age). If that were true, the Western roses would have high genetic diversity and many unique genes. Instead, they have low diversity, suggesting they arrived more recently, likely from the East, rather than from a long-isolated southern pocket.

The Verdict

The paper concludes that the French Rose's current home is a mix of nature and nurture.

Nature did the heavy lifting in the South and East, with the species naturally recolonizing Europe after the Ice Age.
Humans were the key players in the West, particularly in France. The intense breeding of roses in France during the 19th century led to varieties escaping gardens and mixing with wild populations.

The authors are confident about the clonal matches (finding wild plants that are genetic twins of garden ones) but remain cautious about the exact timing of the Western colonization. They suggest it happened relatively recently, possibly through a mix of natural dispersal with a few founders and human planting, but they can't say for sure which one happened first. The study doesn't prove a single "origin story" for the whole species but rather reveals a complex tapestry where nature set the stage, and human gardeners wrote the final act for the roses in the West.

Problem Statement
Rosa gallica L. (the French rose) is a tetraploid, heterozygous species with a complex evolutionary history involving both natural seed propagation and vegetative reproduction via root suckers. While historically significant as a parent to many Old Garden Roses (OGR) and extensively cultivated in 19th-century France, the origins of its wild populations remain unclear. Previous hypotheses regarding its distribution range from natural post-glacial recolonization from southern refugia to human-mediated dispersal during the Roman era or the Middle Ages. However, these hypotheses have not been rigorously tested using molecular data across the species' entire range. Existing genetic studies have been limited to local or regional scales, hindering a comprehensive understanding of the evolutionary factors shaping its current distribution, particularly the interplay between natural recolonization and human activity in France.

Methodology
The study employed a range-wide sampling strategy, collecting leaf samples from 905 R. gallica individuals across 223 sites in 15 countries, alongside 402 suspected related rosebushes (cultivars and botanical varieties) and 259 individuals from other Rosa species. The researchers utilized a recently developed SSRseq (sequence-based microsatellite) genotyping system targeting 60 nuclear SSRs.

Key methodological steps included:

Genotyping and Ploidy Determination: Using Illumina iSeq100 sequencing, the team processed 1,710 samples. Due to the heterogeneity of sample conditions and the inability to perform flow cytometry on all samples, a supervised Random Forest machine learning model was trained on 194 individuals with known ploidy levels to predict the ploidy of the remaining samples (diploid, tetraploid, or hexaploid).
Data Filtering: A rigorous pipeline was implemented to handle missing data, detect null alleles, and identify paralogous loci. Clonal lineages were detected using a threshold-based Euclidean distance method adapted for polyploids, retaining one representative per lineage to create a "clone-corrected" dataset.
Hybrid and Misidentification Detection: To ensure the analysis focused strictly on R. gallica, the researchers used Principal Coordinates Analysis (PCoA) based on k-mer dissimilarities and Discriminant Analysis of Principal Components (DAPC) to identify and exclude interspecific hybrids and misidentified specimens.
Population Structure Analysis: The final dataset of 519 confirmed R. gallica individuals was analyzed using multivariate methods (PCA, PCoA) and Bayesian clustering (STRUCTURE) with the KFinder algorithm to determine optimal cluster numbers ( $K$ ). Differentiation was assessed using the $\rho$ statistic (an analogue of $F_{ST}$ for polyploids), and spatial genetic structure was analyzed using community detection algorithms on spatial graphs.

Key Contributions and Results

Genetic Structure: The study revealed a highly structured genetic landscape. While populations in the South Alps and Central/Eastern Europe were largely assigned to two dominant genetic clusters (suggesting a shared demographic history), French populations exhibited significantly higher complexity, distributed across seven distinct genetic clusters.
Recolonization Patterns: The genetic diversity patterns in South Alps and Central Eastern Europe (high allelic richness, low differentiation between adjacent regions) are consistent with natural post-glacial recolonization from a single southern refugium, likely the Italian peninsula. In contrast, populations in Western and Central France showed lower allelic richness and higher differentiation, suggesting a more recent colonization event.
Human-Mediated Dispersal: The detection of 36 sites containing individuals belonging to the same clonal lineage as cultivated or botanical specimens provided direct evidence of human-mediated dispersal. This was particularly prominent in France, where 28 of the 98 studied sites contained wild individuals clonally linked to cultivars. The largest clonal lineage (Lineage B) spanned 13 sites in Central and Western France, linking wild populations to specific cultivars like 'Rosiers des parfumeurs'.
Western France Origins: The low private allelic richness in Western France contradicts the hypothesis of an ancient, isolated Iberian refugium. Instead, the data supports a scenario where Western populations were established more recently, potentially through founder effects from Eastern populations, followed by human-mediated dispersal that introduced cultivated genotypes into the wild.

Significance
This study provides the first near range-wide characterization of R. gallica genetic diversity. It demonstrates that the species' current distribution is the result of a dual history: natural post-glacial recolonization shaped the broad genetic structure of Central and Eastern Europe, while human activities played a decisive role in the recent dispersal and establishment of populations in Western Europe, particularly France. The findings challenge the notion of a single, ancient natural origin for all European populations and highlight the difficulty in distinguishing between "feral" populations (escaped from cultivation) and indigenous wild populations without molecular data. The research underscores the necessity of integrating genetic analysis with historical records to understand the evolutionary trajectories of horticultural species that have persisted in the wild for centuries.

The Great Rose Mystery: Nature's Journey vs. Human's Garden

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