Solanaceae is the flagship system of our evolutionary biology and systematics research.
We use the nightshade family (Solanaceae)—including tomatoes, potatoes, peppers, and their wild relatives—as a primary model to study evolutionary diversification, phylogenetic relationships, and trait evolution across deep and recent timescales. With ~2,700 species spanning wild and cultivated lineages, Solanaceae offers exceptional taxonomic breadth for addressing fundamental questions in plant systematics and evolutionary biology.
Our work is grounded in natural history collections, particularly herbaria, which provide a temporal framework for reconstructing evolutionary histories and tracking lineage change through time. By integrating herbarium-based sampling with genomics, phylogenomics, and other omics approaches, we resolve species boundaries, infer biogeographic histories, and examine how evolutionary processes respond to environmental change. Through this integrative, collection-driven framework, we link classical systematics with modern evolutionary genomics to understand how biodiversity is generated and maintained.
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Understanding how biodiversity evolves is essential for conserving ecosystems and ensuring sustainable use of natural resources. This project investigates the evolutionary history of a group of plants in the nightshade family known as Physalideae, which are recognized by their distinctive inflated fruits. By combining information from plant fossils, historical herbarium specimens, and modern DNA-based omics technologies, the project explores how key biological traits emerged and how they influenced the spread and diversification of these plants over millions of years.
Collaborators:
Stacey D. Smith & Malia Santos (University of Colorado Boulder, USA)
Isabel Sanmartin, Real Jardín Botánico, CSIC, (Spain)
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This project investigates the evolutionary history of the Morella clade within the Solanum genus, a globally distributed group of nightshade plants that includes important African leafy vegetables and close relatives of major crops such as tomato and potato. Species boundaries in this group remain unclear due to hybridization, polyploidy, and subtle morphological variation. Using DNA extracted from herbarium specimens, the project applies genomic and bioinformatic approaches to reconstruct complex evolutionary histories and uncover hidden species diversity, particularly within Solanum nigrum. The results will improve plant classification, support crop breeding and conservation, and demonstrate the value of museum collections for modern genomic research.
Collaborators: Tiina Särkinen (RBGE, Scotland, UK), Sandy Knapp (NHM, UK)
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This project explores how wild tomatoes evolved as they spread across the northern Andes, one of the most biologically complex regions on Earth. By studying DNA from different parts of the cell, the research investigates how some tomato species carry genetic “signatures” of past hybridization with other species. Focusing on wild relatives of cultivated tomato, the project links these genetic patterns to movement through the Amotape–Huancabamba Zone, a natural crossroads of climates and landscapes. The project explores how hybridization and geography drive plant diversity and provides valuable knowledge for conserving wild tomatoes and improving future crop breeding.
Collaborators: Patricia Bedinger, Amanda Broz, Dan Sloan (University of Colorado Boulder, USA)
This project explores the evolutionary history of the Browallieae tribe, a group of nightshade plants found from the high Andes to Central America. These plants show striking diversity in form, chemistry, and habitat, yet their relationships remain poorly understood. Using modern genomic tools, the research reconstructs evolutionary relationships across the group to clarify species boundaries and uncover how diversification shaped their evolution. The results will improve plant classification, support conservation of threatened species, and highlight the potential of Browallieae for horticultural and pharmaceutical applications, contributing to a more complete understanding of plant biodiversity in the Americas.
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This project explores how wild potato species evolved through hybridization and gene exchange in South America. Focusing on three closely related wild potatoes that grow side by side, the research combines plant morphology, geography, and modern DNA sequencing to understand how species boundaries form—and blur—over time. By uncovering the evolutionary history of these wild relatives, the project helps resolve long-standing taxonomic questions and identifies genetic traits linked to disease resistance and environmental stress tolerance. The results will support conservation of wild potato diversity and provide valuable genetic resources for developing more resilient cultivated potatoes.
Collaborators: Gustavo Heiden (Embrapa Clima Temperado, Brazil)
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This project explores the evolutionary history and diversity of Limonium (sea lavenders), a species-rich plant group known for its striking coastal flora and high levels of endemism. Limonium species are especially diverse in Mediterranean and island regions, where complex evolutionary processes such as hybridization, polyploidy, and adaptation to extreme environments have generated remarkable diversity. Using modern DNA sequencing approaches, the project integrates genomic data from living and historical plant material to clarify species boundaries, reconstruct evolutionary relationships, and trace patterns of diversification and dispersal. By resolving long-standing taxonomic and evolutionary uncertainties, the research contributes new insights into plant evolution and provides knowledge relevant to biodiversity conservation and the sustainable management of fragile coastal ecosystems.
Collaborators: Nunzio D'Agostino, University of Naples Federico II (Italy)
This project focuses on Forsteronia, a group of tropical climbing plants native to the Neotropics that play important ecological roles in South American forests but remain poorly understood from an evolutionary and taxonomic perspective. Despite their distinctive flowers, fruits, and growth forms, species of Forsteronia have not previously been studied using modern genomic approaches, and their classification has remained outdated. By combining fieldwork in Brazil with extensive research in herbaria across South America and Europe, the project integrates historical specimens with newly collected material. Using state-of-the-art DNA sequencing, including genome-scale data from preserved museum samples, the research reconstructs evolutionary relationships, clarifies species boundaries, and traces biogeographic history. The project will deliver updated taxonomic tools, distribution data, and conservation-relevant insights, highlighting the value of natural history collections for modern evolutionary research.
Collaborators: Ingrid Koch (Universidade Estadual de Campinas, Brazil), Rafaela Jorge Trad (RBGE, Scotland, UK)
Our ongoing research explores plant–microbiome associations using herbarium specimens as molecular records of past ecological interactions. By analyzing DNA preserved in historical plant collections, we investigate not only plant genomes but also diverse microbial communities associated with leaves, stems, and reproductive tissues. These preserved microbiomes allow us to study long-term patterns that cannot be captured using modern samples alone.
Using high-throughput sequencing, we examine how plant-associated microbial communities are shaped by host identity, geography, and environmental conditions. A key focus is identifying which microbiome components remain stable through time and which respond to environmental change, land use, or pathogen emergence. By integrating museomics with microbiome research, this work highlights the value of natural history collections for understanding the structure and dynamics of plant–microbe interactions across historical timescales.
This research uses herbarium specimens as historical genomic records to investigate the origin and evolutionary history of Peronospora sparsa, with a focus on the dryberry disease outbreak that affected Rubus populations in Finland during the 1990s. By combining historical DNA from preserved specimens with modern evolutionary genomics, we examine how the pathogen’s genetic diversity, geographic distribution, and host associations have changed through time. A key aim is to identify genomic signatures linked to host shifts and adaptation, placing disease emergence in a long-term evolutionary framework. This collection-based approach highlights the value of herbaria for studying pathogen evolution and host–pathogen interactions across historical timescales, with implications for understanding and mitigating future disease outbreaks.
Collaborators: Hanna Susi
Funding: AGFOREE Doctoral School Grant
The history of a science is often as instructive as science itself. As we study how other people have made scientific breakthroughs, we develop the breadth of imagination that would inspire us to make new discoveries of our own. Natural history museums grew out of early “cabinets of curiosities,” built from collections of prints, handwritten documents, rare books, and specimens gathered from across the natural world. These archival collections are an unparalleled resource for historians, researchers, artists, and scholars. Specimens acquire meaning through the people, places, and practices they encounter on their journey into museum collections, linking natural history museums to broader scientific and civic cultures. Archival records reveal how specimens were classified, analysed, and displayed, embedding scientific practice in material culture. Using these archival materials, this project investigates early nineteenth-century ideas of biological inheritance, a period when heredity was understood first as an abstract force and later as a material and morphological problem. Debates about heredity addressed relationships between generations, environments, and biological diversity, while also resonating with wider discussions about citizenship, progress, decline, and tradition—questions that remain highly relevant today.
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Research led by Hosein Ahmadi (2024–2025)
This study investigated the molecular mechanisms underlying chemical diversity in Thymus daenensis, a wild thyme species valued for its essential oils and medicinal properties. The research focused on two metabolically distinct genotypes characterized by contrasting levels of the bioactive compounds thymol and carvacrol—key constituents responsible for thyme’s aroma and therapeutic value.
Using high-throughput RNA sequencing, gene expression profiles were analyzed during the flowering stage, when essential oil biosynthesis is most active. The analysis identified hundreds of differentially expressed genes between the two chemotypes, including enzymes and transcriptional regulators involved in terpene biosynthesis pathways. These results reveal how shifts in gene expression contribute to variation in secondary metabolite production at the molecular level.
By linking transcriptomic variation to chemical traits, the study provides new insights into the regulation of plant metabolic pathways and the genetic basis of phytochemical diversity. The findings have practical implications for breeding aromatic plants, conserving wild genetic resources, and improving the sustainable use of medicinal species. More broadly, this work demonstrates how modern omics approaches can uncover the genetic foundations of economically and ecologically important plant traits.