Welcome to the Joly Laboratory!

Our laboratory aims at understanding biodiversity by studying plant evolution. Our research involves field work, molecular biology, and uses analytic and modelling approaches. We use tools from phylogenetics, population genetics, quantitative genetics and bioinformatics to understand the evolutionary processes that were involved in shaping the diversity of plants.

The main subjects studied in the laboratory are the evolution of reproductive systems, plant adaptation to their environment, speciation, hybridization, and plant genetics.

Lab news

Outreach prize for Marion Leménager

At the last Acfas congress, Marion Leménager was awarded a favorite's prize in the Acfas outreach competition. Marion presented a comic strip describing her work on the evolution of flowers in 3D that stood out for her originality. The comic strip entitled Flowers not at all flat can be viewed on the Acfas website.

Studying flowers in 3D

Marion Leménager has just published a protocol to reconstruct 3 dimensional flower models using photogrammetry. This approach is more affordable and easier to use than conventional laser methods. She shows in the paper how the method can be used to study flower evolution. The protocol is freely accessible and everyone can contribute to improving it.

Here is a model of Rhytidophyllum vernicosum built with this method:

Check out our SketchFab collection for other models.

Heliotropism in Trillium grandiflorum provides increased reproductive success

A study lead by Maryane Gradito described for the first time heliotropism in the white trillium. Heliotropism is the propensity of organs (here flowers) to follow the sun. She also showed that heliotropism provides individuals with a reproductive advantage, increasing the proportion of ovules that get fertilized. The paper is available in open access. And here is a stop motion video of white trilliums over a whole day:

The work of Gonzalo Bilbao on the cover page of the American Journal of Botany

The work of Gonzalo Bilbao on the evolution of petal shapes of Erythrina was featured on the cover page of the September issue of the American Journal of Botany. Gonzalo's work showed that 2D petal shapes can infer pollination modes pretty accurately in the legume genus Erythrina. Interestingly, although much attention has been given to the standard petals as a predictor of pollination strategies in Erythrina in the past, the results show that the shape of the wings and particularly the keel petals contain information that helps infer pollination modes. The full details can be read here.

The production of closed flowers: Darwin was right

Some plants produce to types of flowers: normal open flowers and small flowers that never open. The latters are called cleistogamous flowers and the phenomenon is called cleistogamy. This amazing capacity is not common, but it is relatively widespread being found in more than 40 plant families and it represents a nice example of convergent evolution. Darwin proposed the hypothesis that cleistogamy evolves more frequently in species with bilaterally symmetric flowers (one plane of symmetry, like the flowers of orchids and violets). This is because cleistogamy ensures pollination in the absence of pollinators and that bilaterally symmetric flowers are typically pollinated by fewer species than radially symmetric flowers (multiple planes of symmetry, like roses or daisies) and are thus more likely to fail pollination. Using a dataset of more than 2500 species, Simon Joly and Daniel J. Schoen (McGill) confirmed Darwin's hypothesis. The full details can be read in Current Biology.

Congratulation Dr Julie Faure

Dr. Julie Faure successfuly defended her Ph.D. thesis on December 16th 2020. Her thesis investigated the adaptation of flowers to their pollinators. The title, in French, is "Adaptation florale aux pollinisateurs : étude des Gesneriaceae antillaises et de l’Impatiente du Cap". Congratulations Julie and good luck for the next steps!

How to reproduce following an Hurricane?

Julie Faure has just published the first chapter of her thesis that reports pollination information for the endemic species Rhytidophyllum bicolor in Haiti. The interesting thing about this study is that it was conducted 15 months following the passing of the Matthew Hurricane in Haiti in 2016. Rhytidophyllum bicolor, a pollination generalist, continues to be pollinated by bats and bees even if hummingbirds populations were almost completely eradicated by the Hurricane.

New multi-platform package to model the evolution of traits and their variances

In this recent study conducted with Swiss, New Zealand and Swedish colleagues, we present a new multi-platform package (R, BEAST2) that allows to model the evolution of traits and their variances. This package has several improvements over the original one, including greater comutational efficiency, availability of more models, and the possibility to jointly estimate the phylogeny in BEAST2.

Study on tree genetics and climate warming out

In a new study made in collaboration with Elizabeth Wolkovich (UBC), we showed that taking into account phylogenetic relationships and genetic similarities within species allows to get more precise results in multi-species studies. We applied the approach to a climate change study on 10 tree and shrub species and show that considering the genetic of individuals within species allows to better predict the reaction of plants to climate changes.

Welcome to Maryane Gradito

We are happy to welcome Maryane Gradito, an NSERC BRPC summer intern in the lab who will work on the reproduction of the white trillium.

Willow holobiont paper is out!

In this paper, we present metatranscriptomic results of willow roots and show that plants that have grown in contaminated soils not only demonstrate altered plant gene expression, but also shifts in fungi and bacteria communities associated with the roots. These results show that it is important to consider not only the plant, but also its associated microbes when studying an organism response to its environment. It is the holobiont concept.

New grant to study wheat adaptation to drought

We are happy to announce that we obtained a NSERC Strategic grant to study the adaptation of wheat to drought conditions. The project is lead by Etienne Yergeau from the Armand-Frappier Institute (INRS) and is done in collaboration with the compagny Kopert, Philippe Contant of the INRS and Marc St-Arnaud of the Montreal Botanical Garden. The project will investigate the potential of the wheat microbiote, and also epigenetics, to allow rapid adaptation of wheat to drought conditions.

Congratulations to Marie Florence Sandrine NGO NGWE

Sandrine Ngo Ngwe, who sucessfully defended her Ph.D. thesis last summer in Yaounde, Cameroon, has just been named head of the National Cameroon Herbarium. Congratulations Sandrine on this great achievement!

Congrats to Dr Alexandre!

Congratulation to Hermine Alexandre who just defended her Ph.D. thesis. Hermine is starting a postdoc in Bordeaux, France, in January. It was a pleasure to have you around the lab these last four years!

Explaining plant naturalization and invasiveness

Simon Joly contributed to a study recently published in Ecology and Evolution that proposes models to explain which plants are more likely to become naturalized or invasive in Quebec. Plant attributes were used as explanatory factors but also propagule pressure, which was inferred from old plant catalogues, scientific publications and herbarium specimens. The results showed that plant hardiness is important for naturalization, but to become invasive plants also need good dispersal qualities.

Congratulations to Gonzalo!

We are very happy for Gonzalo Bilbao who has just received the prestigious Spanish Caixa fellowship. Well done!

New R package

Publication of the new R package pofadinr that implements the genetic distances genpofad and matchstates. These recently described methods are very efficient for estimating genetic distances among individuals. They are particularly useful for genomic data (SNPs) and they can be used with both hybrids and polyploids.

Welcome to Julie Faure

The Joly lab welcomes Julie Faure who is starting a Ph.D. on pollination in Antillean Gesneriaceae and its impact on the evolution of the group.

Diversity and evolution of yams in Cameroon

Sandrine Ngo Ngwe has just published a paper that discusses the evolution and diversity of yam species (Dioscorea ssp.) of Cameroon. She showed that wild species have a stronger genetic structure than wild species, potentially because of agricultural practices that favour gene flow between regions. She also showed that most species are not monophyletic.

Biotic cross-tolerance in willow trees revealed by meta-transcriptomics

This article originating from the GenoRem project has just come out in BMC Plant Biology. Many lab members have contributed, notably Emmanuel Gonzalez, Nicholas Brereton and Julie Marleau. The study reports meta-transcriptomic (gene expression) results of willows in a phytoremediation context. It shows that many willow genes are differentially expressed between contaminated and non-contaminated treatments. But the most interesting results are that genes from other organisms were also extracted from the plant tissues and were found to be differentially expressed. This is the case of spider mite genes. These spider mites have preferentially infested the trees growing in non-contaminated soil. We suggest that this is due to a cross tolerance effect induced by the soil contamination. This inter-kingdoms gene expression investigation was made possible by the developpement of a novel bioinformatic pipeline that is descripbed in the paper.

New paper on the genetic architecture of pollination syndrome transitions

This new paper by Hermine Alexandre published in PeerJ describes the genetic bases involved in a pollination syndrome transition from a pollination generalist to a pollination specialist in Rhytidophyllum. A QTL analysis has shown that flower color changes were due to a single gene whereas floral shape variation are determined by a few genes each with a moderate effet. These results show that important morphological changes can be caused by a small number of genes.

Laurent De Vriendt has made his final thesis submission

Congratulation to Laurent who has successfully obtained his M.Sc. degree from Laval University! Laurent has made a superb contribution on the impact of isolation on phenetic and fitness traits on an emblematic orchid of Quebec peatlands, the white-fringed orchid.

The correlation between phylogenetic diversity and functional diversity over evolutionary scale

Have a look at this paper co-authored with Alain Paquette and Christian Messier that investigates the link between phylogenetic diversity and functional diversity over evolutionary scale.

Welcome Gonzalo Bilbao

We are very happy to welcome Gonzalo Bilbao, co-supervised by Anne Bruneau, who will study the evolution of pollination syndrome evolution in Erythrina (Fabaceae).

New recruits

We are happy to welcome Louna Fronteau and Julie Faure, who are comming to do their Master II internship in our lab. Louna will work on the genetic bases of the loss of red pigments in Rhytidophyllum flowers, whereas Julie will work on the importance of plant-pollinator interactions in predicting the distribution of Gesneria and Rhytidophyllum species.

New SNP-based distances measures

Check out this preprint manuscript describing new distance methods from SNP data. They are particularly useful in the presence of allelic variation, recombination and polyploidy. They are implemented in POFAD.

Back from field trip in Haiti

Simon Joly and François Lambert are back from a field trip in Haiti, where they collected Gesneria viridiflora as well as several other Gesneria and Rhytidophyllum species.

Paper on evolution by niche shifts out!

This paper presents an approach to test for adaptive radiation by comparing the environmental disparity through time plots to expectations from Brownian and niche shifts models. The approach is tested on the genus Pachycladon that radiated in the Southern Alps in New Zealand in the last million years.


Simon Joly

Institut recherche en biologie végétale
4101 Sherbrooke East
Montréal, QC H1X 2B2

+1 514.872.0344