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Institut für Systematische und Evolutionäre Botanik


My research revolves around the following fundamental questions in evolutionary biology: How is biological diversity partitioned at different temporal, spatial, and genomic scales? What are the processes that generate and eliminate biological diversity? How do geography, ecology, and genomes shape the evolution of biological diversity? I strive to address the complexity of these questions by integrating evidence at different evolutionary scales and using a variety of methodological approaches, ranging from phylogenomics and biogeography to population genomics and phylogeography, from comparative genomics to reproductive biology and morphometrics, pollination and field experiments, and incorporating demographic, ecological, and evolutionary modeling.

Within the framework of the overarching questions outlined above, I pursue two main lines of research that intersect with each other at several conceptual and methodological levels: 1) Evolutionary biology of heterostyly and primroses (Primula L., Primulaceae); 2) Biogeography in the Mediterranean realm, with emphasis on the origin of plants endemic to oceanic and continental islands. See current projects of members of Conti’s lab


Evolutionary genomics of the heterostyly supergene in Primulaceae

Heterostyly, a floral polymorphism that promotes outcrossing and is controlled by a supergene (the S-locus), evolved repeatedly in flowering plants and has been the subject of intensive research ever since Darwin’s seminal work on primroses (Primula). Recent studies, including our own in Primula, have started to characterize the molecular basis of this complex floral syndrome and have generated genomic resources that are essential for further progress on the genetic control of heterostyly. Key questions that remain unanswered are:

  1. Which molecular processes drive the assembly, evolution, and loss of the S-locus?
  2. Does introgression affect the S-locus?
  3. How do homostylous taxa originate from heterostylous ancestors?

We address these questions via comparative genomic and phylogenomic analyses of newly assembled, high-resolution genomes from heterostylous and homostylous relatives throughout Primulaceae (i.e., in Primula, Hottonia, and Androsace). This strategy will allow us to test alternative hypotheses about the origin, evolution, and loss of heterostyly at different time scales in Primulaceae.

The evolutionary roles of hybridization and introgression: investigating species and genomic boundaries under climate change (Primula genomics: PrimGEN)

Some of the most fundamental questions in evolutionary biology concern the nature of species boundaries and hybridization: What allows species to exchange genetic information and what keeps them apart? Which parts of their genomes are differentially affected by introgression and why? These key questions have become even more important in the face of the staggering changes to the natural environment caused by human activities. However, progress in understanding how genetic exchange between hybridizing species shapes the structure and distribution of biological diversity has been hampered by a lack of: (a) comparisons at different temporal and geographic scales and (b) integration of genomic data with ecological and demographic models, insufficient sampling, and inadequate genomic and analytical resources, precluding inferences at fine resolution. Therefore, we aim at improving our understanding of the evolutionary roles of introgression and hybridization by: (i) integrating phylogenomic, population genomic, and modeling analyses at multiple temporal and geographic scales among Primula species that hybridize at different frequencies; (ii) performing high-resolution, comparative analyses of whole genomes between hybridizing species of Primula sect. Primula. In particular, we will focus on the effects of hybridization on the genomic region that controls heterostyly, a reproductive system characterized by the balanced occurrence of different individuals with reciprocally placed male and female sexual organs.

This study on plants characterized by a hermaphroditic, heteromorphic reproductive system controlled by a hemizygous supergene, as opposed to systems characterized by distinct sex chromosomes (more frequent in animals than plants), will provide novel insights on how hybridization differentially affects plants vs. animals and on the function and evolution of supergenes.

Plant reproductive biology

In plant reproductive biology, I am integrating data from phylogenies, phylogeography, molecular cytogenetics, floral morphology, and pollination experiments to study the relationships between plant mating strategies, ploidy levels, and speciation. For this part of my research program, I am focusing on Primula, a highly diverse, circumboreal genus that includes both heterostylous (i.e., with two, genetically determined floral morphs that differ in the reciprocal position of sexual organs) and homostylous (i.e., with only one floral morph) species and ploidy levels that vary from diploidy to 14-ploidy. Phylogenies allowed my post-doc Austin Mast and I to establish that the ancestor of all 430 extant species of Primula was heterostylous, while homostyly was secondarily derived in all cases (Mast et al., 2001, 2006; Mast and Conti 2006) and that the buzz-pollinated species of Dodecatheon originated from within the heterostylous Primula (Mast et al., 2004; studies funded by a grant of the Swiss National Science Foundation). By comparing evidence from nuclear and chloroplast DNA sequences, and chromosome in situ hybridization analyses, my Ph.D. student Alessia Guggisberg and I were also able to determine the parental origins of several polyploids in Primula sect. Aleuritia, to conclude that switches to homostyly occurred exclusively in polyploid lineages, which mainly occupy previously glaciated areas, and to propose that the higher success of the autogamous polyploid species at recolonizing habitats freed by glacial retreat might be explained in terms of selection for reproductive assurance (Guggisberg et al., 2006, 2008, 2009). Recently, with my Master student Laura Granato, I also used flow cytometry, in combination with molecular phylogenetic analyses of chloroplast and nuclear DNA sequences, to investigate the origins of different ploidy levels in Primula marginata. As with my research on biogeography, I have been invited to present the results of my work on the evolution of plant reproductive strategies and ploidy levels in Primula at several departmental and conference talks in China, the USA, Italy, Switzerland, South Africa, Slovakia, Brasil, and the UK and my students have contributed oral and poster presentations on the same topics at several international conferences in Europe (Italy, France, Switzerland, Netherlands), the USA, Canada, Australia, and New Zealand. My current and future research projects focus on asking whether (i) the evolution of heterostyly was the main driver of increased diversification rates in Primulaceae, (ii) variation in anther-stigma separation in homostylous species affects selfing rates, and (iii) the interaction between floral morphology and pollinators contributes to modulating gene flow between hybridizing species of Primula (with Ph.D. student Jurriaan de Vos and post-doc Barbara Keller). To quantify the relationships between sexual organ position, pollen transfer, and plant reproductive fitness I am adding experimental components that entail flower, fruit, and seed trait measurements, controlled pollination experiments in flight cages, and floral bagging experiments to exclude pollinators. Additionally, I started a collaboration with Ben Haller, a Ph.D. student at McGill University, to model the role of heterostyly in pollinator-driven speciation. After a first visit to Zurich in Fall 2010, Ben Haller will spend two weeks in February 2011 with me and two of my students (Jurriaan de Vos, Barbara Keller) to refine the details of the model. The next key steps in shaping my future research strategies on hybridization and the evolution of breeding systems in Primula will focus on developing comparative genomic approaches based on Single Nucleotide Polymorphisms and attempting to characterize the main genes that control the two main components of heterosytly: i) reciprocal herkogamy (i.e., the reciprocal positioning of sexual organs in the two floral morphs) and ii) self- and intra-morph pollen incompatibility. The availability of a new position as Oberassistant in my research group presents a unique opportunity to hire a scientist with research expertise that optimally complements mine and address the evolution of reproductive strategies in Primula from molecular genetic, developmental, and evolutionary perspectives.


In biogeography, I have used both phylogenetic/phylogeographic, population genetic, and molecular cytogenetic approaches to investigate: the origin of Alpine taxa (Conti et al., 1999); the role of refugia in the survival of Alpine endemics (for ex., in the rare Saxifraga florulenta; Szövényi et al., 2009); the link between secondary contact after glacial retreat and allopolyploid speciation during the Pleistocene (Guggisberg et al. 2006, 2008, 2009); the role of geological events in shaping patterns of distribution both in Southeast-Asian (Conti et al., 2002 and 2004; Rutschmann et al. 2004, 2007) and Mediterranean plants (Mansion et al. 2008, 2009; Salvo et al., 2008, 2010) from the Cretaceous to the Tertiary; and, currently, whether island colonization is linked with changes of genetic diversity and ecological preferences.

An important component of my recent work on biogeography has focused on the Mediterranean Region sensu lato (extending to the Macaronesian archipelago) because this area, including both continental fragment (e.g., Corsica and Sardinia) and oceanic islands (e.g, the Canarian archipelago), provides an ideal setting to compare the influence of island origin on processes of colonization and speciation. Ever since Darwin’s seminal chapters on geographical distribution in “The origin of species” (1859), islands have played a key role in the development of biogeographic theory. One aspect that has not been sufficiently studied concerns the role of different geologic origins (e.g., continental fragment vs. oceanic islands) on evolutionary dynamics. Fragment islands, which were once part of continental plates, already harbored a full set of co-adapted communities when they separated from the mainland. Conversely, when oceanic islands emerged from the bottom of the ocean and for some time thereafter, they harbored either no or only a few species. Fragment islands may be colonized via range expansion prior to plate separation, migration over temporary land bridges, or long distance dispersal following fragmentation, while oceanic islands may be colonized exclusively via long distance dispersal. The availability of open ecological niches at island birth also differs between fragment and oceanic islands, with an important temporal dimension attached to this factor (i.e., niche filling over time in oceanic islands).

Recent improvements in molecular dating and ancestral area reconstruction methods, integrated with knowledge of paleogeography, paleoclimatology, and plant ecology, now allow us to infer the relative roles of past geologic (i.e., microplate movements, formation of temporary land corridors, island formation) and climatic events (i.e., onset of the Mediterranean climate) vs. stochastic processes (i.e., long distance dispersal) in the colonization of continental and oceanic islands. In my studies, I compared the origins of fragment and oceanic island endemics in Mediterranean Araceae (Mansion et al., 2008), Boraginaceae (Mansion et al., 2009), and Rutaceae (Salvo et al., 2008, 2010, 2011). The results supported the single colonization of the Canarian archipelago, followed by in situ diversification, by both Echium (Boraginaceae) and Ruta (Rutaceae) during the Miocene, likely after the formation of the oldest island (Fuerteventura) about 20 Mya and well before the onset of the Mediterranean climate in the Pliocene. Additionally, the colonization of islands within the archipelago does not appear to conform to the classic stepping-stone model in Ruta. The origin of Corso-Sardinian endemics is likely explained by the fragmentation of the Hercynian mountain belt in the early Oligocene for Helicodiceros muscivorus (Araceae), by the separation of the Corso-Sardinian microplate from the Apulian microplate in the middle Miocene for R. lamarmorae, R. corsica (Rutaceae), and A. pictum (Araceae), by temporary land connections with neighboring landmasses during the Messinian Salinity Crisis of the late Miocene for Borago, and by long distance dispersal during the Pliocene for Anchusa (Boraginaceae). Altogether, the studies I led with my Ph.D. student (G. Salvo), post-doc (G. Mansion) and collaborators highlight the key roles of both tectonic and eustatic processes of marine transgression-regression for the origin of endemics in the continental fragment islands of Corsica and Sardinia and the importance of identifying discrete time windows for colonization for the origin of endemics in the oceanic Canarian archipelago.

The recent work on the biogeography of Mediterranean islands was supported by two grants of the Swiss National Science Foundation, one to fund the Ph.D. student and post-doc mentioned above and one (together with other grants) to fund an international conference entitled “Origin and evolution of biota in Mediterranean climate zones: an integrative vision” (Institute of Systematic Botany, University of Zurich; July 14-16, 2007; 130 participants from 12 countries in Europe, North America, South America, and Australia). I also convened a special issue on Mediterranean biogeography in the International Journal of Biogeography (IF 4.566; July 2009), which included 13 peer-reviewed studies initially presented at the conference. Additionally, my post-doc, Ph.D. student, and I were invited to present our results on Mediterranean biogeography at 13 international conferences (France, Italy, Spain, Switzerland, USA, Mexico, Japan, Australia, Indonesia), contributed presentations at 7 meetings of scientific societies (Mexico, Switzerland, Spain, USA, Austria) and gave talks to the general public (e.g., Tuesday Garden Tours at the University of Zurich).

After incorporating geological, climatological, and evolutionary biological knowledge within a phylogenetic framework to provide temporal and spatial scenarios for the origin of island endemics, the current challenge is to add population genetic and ecological niche modeling dimensions to further elucidate the processes of island colonization. Thus I recently started to supervise a project with Dr. Marilena Meloni (recipient of a Marie Heim Voegtlin grant from the Swiss National Science Foundation to work in my research group) aimed at testing whether island colonization causes genetic bottlenecks by comparing the genetic diversity of island endemics and widespread relatives of Ruta. The first results will be presented at two international conferences in Berlin and Melbourne in 2011. I am currently starting another project with Dr. Ares Jimenez, a post-doc in my lab, aimed at investigating whether island colonization is associated with a reduction of genetic diversity, switch to selfing reproductive strategies (i.e., testing Baker’s law), and change of ecological preferences in Canarian endemics of Limonium, a genus characterized by both floral dimorphism and heterostyly (see below) in widespread, mainland relatives. While Dr. Jimenez is the person who is developing the details and will write a research proposal to appropriate funding bodies, I am looking forward to supervise his work because it will allow me to merge my interests in plant breeding systems and biogeography. Along the same lines, I am convening a symposium entitled “Past, present, and future of island plants: evolutionary, niche modeling and conservation perspectives” to foster an innovative, synergistic vision on the origin, evolution, and future prospects of island floras. My symposium proposal has been accepted by the organizing committee of the 18th Botanical Congress (Melbourne, Australia, July 23-30, 2011) and will bring together scientists with different kinds of expertise and perspectives on island biogeography.

The other main current and future direction of my work in biogeography entails the explicit merging of ecological niche models into a phylogenetic framework to explore how plant ecological preferences and distributional ranges vary through time and how they are affected by changing climates. In this case, I am focusing my research on alpine/arctic regions, because several studies have shown that they are among those most endangered by global warming and because high-resolution paleoclimatological data are available for the Pleistocene glacial cycles of Europe. In collaboration with Dr. Christoph Randin (University of Basel), an expert in niche modeling, I am building on my previous phylogenetic and population genetic results in Primula sect. Aleuritia (Guggisberg et al. 2006, 2009) and Saxifraga florulenta (Szovenyi et al. 2009) to (i) test the model of allopolyploid speciation by secondary contact and whether island colonization is associated with a switch of ecological niche and from heterostyly (an obligate outcrossing reproductive strategy) to homostyly (a selfing reproductive strategy) in Primula; and (ii) investigate whether the phylogeographic history, genetic diversity, climatic niche and dispersal mode of S. florulenta can explain its long persistence in the Maritime Alps, a hot spot of biodiversity, and predict its future survival or extinction on mountain tops. This project, funded by the Swiss National Science Foundation, will officially start with the arrival of two Ph.D. students, Spyros Theodoridis and Theofania Patsiou, at the University of Zurich on February 1, 2001. I would like to continue to explore the connections between Pleistocene glacial cycles, plant distributional ranges, phylogenetic/phylogeographic relatedness, and changes in ecological preferences though time in the primroses of China, the main center of species diversity for the genus. An extended visit with Prof. Liu (Lanzhou University) in June 2010 has prompted the interest of two current Masters students (Lirui Zhang and Guangpeng Ren) to join my lab by seeking funding through the China Scholarship Council.

Origin and evolution of plant diversity in the Maritime Alps

Collaborators: Karina Arroyo (Master's student), Patrizia Rossi (Parco delle Alpi Marittime); Benoit Laquette (Parc du Mercantour); Giuseppe Vendramin (University of Florence); Giorgio Binelli (University of Vicenza)

Keywords:Maritime Alps, refugia, endemism, molecular dating.

Goals:Reconstruct the phylogenetic relationships of selected endemic species to identify their most likely sister group.

1. Date the origin of endemic species.

2. Compare patterns and temporal sequences of speciation among the selected genera.

The Maritime Alps, straddling the French-Italian border, have been identified as the region with the highest diversity of plant species, and specifically of endemics, in the entire Alpine chain. At the same time, the Alps are massively affected by human-driven changes. For example, human encroachment is significantly curtailing habitat diversity. Global warming is pushing the snow limit up the mountains, reducing habitat space available to high-alpine species. Despite the central importance of the Maritime Alps to understand larger-scale processes of species diversification and assembly in the Alps and in the Mediterranean, no comprehensive studies are available aimed at elucidating the origins of this diversity with current molecular and analytical methods.

One of the explanations provided for the high number of endemics in the Maritime Alps is that this region, which was never glaciated, served as a refugium where some species escaped extinction caused by Pleistocene glacial expansions. Our integrated phylogenetic and molecular dating analyses will allow us to test the proposed refugial nature of the Maritime Alps by estimating the ages of plant species endemic to this region, thus determining whether their origin is pre-Quaternary.

Current and recent research projects


  • Develop reference genome for P. veris with chromosome-level resolution, linkage map, and pangenome, improving on current genome draft with 63% coverage of the 480 Mb genome.
    (Giacomo Potente, Ph.D. student, EU-ITN PlantHUB grant to Conti)
Giacomo Potente
Giacomo Potente
  • Molecular and functional characterization of male genes (anther position, pollen compatibility and size) at the S-supergene, after characterization of female genes (stigma position).
    (Barbara Keller & Giacomo Potente, in collaboration with Prof. Michael Lenhard, Potsdam University)
Barbara Keller
Barbara Keller
  • Elucidate molecular assembly, evolution, and loss of the S-locus in Primulaceae: roles of duplications, translocations, loss of recombination Test whether the S-supergene is hemizygous throughout Primula, beyond P. veris and P. vulgaris.
    (Etienne Leveille-Bourret, Narjes Yousefi: post-docs)
Narjes Yousefi
Narjes Yousefi
Etienne Leveille
Etienne Leveille
  • Hybridization and introgression at different geographic and temporal scales: Which parts of the genome are more or less prone to moving between species? Is the S-supergene affected by introgression?
    (Rebecca Stubbs, post-doc funded by SNF grant to E. Conti)
Rebecca Stubbs
Rebecca Stubbs
  • Are shifts from heterostyly to homostyly associated with shifts from outcrossing to selfing and decrease of genetic diversity? (Emiliano Mora Carrera, Ph.D. student funded by Swiss Government Excellence Scholarship)
Emiliano mora
Emiliano Mora



  • Hybridization, introgression, and reproductive barriers between heterostylous species
  • The role of floral trait variation in speciation of heterostylous groups
  • Developmental variation of breeding systems and mating strategies in homostylous and heterostylous species of Primula
  • Characterization of the heterostyly supergene (with Michael Lenhard, Uni of Potsdam, Germany)
  • Development of genomic and transcriptomic resources in Primula
  • NGS-based phylogenomics of Primula and Limonium
  • Phylogeny and evolution of floral dimorphism in Primulaceae and Plumbaginaceae (Limonium)
  • Biogeography, ploidy levels, and breeding system evolution in Primula


  • The roles of geology, climate and ecology in explaining plant distributions
  • Origin and evolution of island endemics in the Mediterranean Region: comparisons between oceanic and continental islands
  • Patterns and processes of diversification in the Macaronesian archipelagos
  • Phylogeny and biogeography of Mediterranean Boraginaceae, Araceae, Rutaceae
  • Origin and evolution of plant diversity in the Maritime Alps
  • Integrating phylogenetic, niche-modeling, and demographic tools to explain the evolution of Alpine plants

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