Margot Paris

Université de Fribourg · Unit of Ecology and Evolution

In geographically and ecologically heterogeneous landscapes, such as tropical mountains, widely distributed species may be informative proxies for studying landscape and climatic evolution. We explore historical vicariant and dispersal processes that may have determined the genetic structure and variation of a palm species complex living in cloud f...

Biological dispersal is increasingly seen as a primary driver of speciation across the tropical Andes. Similarly, growing evidence suggests that the Northern Andes cordilleras formed as disconnected segments, at least until the late Miocene. For montane species, this discontinuity can hinder dispersal to the different mountain segments. Hence, unde...

Target capture has emerged as an important tool for phylogenetics and population genetics in non-model taxa. Whereas developing taxon-specific capture probes requires sustained efforts, available universal kits may have a lower power to reconstruct relationships at shallow phylogenetic scales and within rapidly radiating clades. We present here a n...

Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome data sets from natural populations of this species have been published over the last years. A major challenge is the integration of disparate data sets, often generated using different sequencing technologies and bioinformatic pipeli...

Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome datasets from natural populations of this species have been published over the last years. A major challenge is the integration of disparate datasets, often generated using different sequencing technologies and bioinformatic pipeline...

Target capture emerged as an important tool for phylogenetics and population genetics in non-model taxa. Whereas developing taxon-specific capture probes requires sustained efforts, available universal kits may have a lower power to reconstruct relationships at shallow phylogenetic scales and within rapidly radiating clades. We present here a newly...

The tropics hold at least an order of magnitude greater plant diversity than the temperate zone, yet the reasons for this difference are still subject to debate. Much of tropical plant diversity is in highly speciose genera and understanding the drivers of such high species richness will help solve the tropical diversity enigma. Hybridization has r...

Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome datasets from natural populations of this species have been published over the last 20 years. A major challenge is the integration of these disparate datasets, often generated using different sequencing technologies and bioinformatic...

This note details the consortium's rationale behind its decision to modify the metadata for putatively misidentified European samples in the DrosRTEC dataset. In brief, we use PCA on published datasets from North America and Europe to generate phylogeographic clusters reflective of worldwide D. melanogaster demography. We used this PCA to train a D...

The adaptive radiation of Bromeliaceae (pineapple family) is one of the most diverse among Neotropical flowering plants. Diversification in this group was facilitated by shifts in several adaptive traits or “key innovations” including the transition from C3 to CAM photosynthesis associated with xeric (heat/drought) adaptation. We used phylogenomic...

Vriesea is the second largest genus in Tillandsioideae, the most diverse subfamily of Bromeliaceae. Although recent studies focusing on Tillandsioideae have improved the systematics of Vriesea, no consensus has been reached regarding the circumscription of the genus. Here, we present a phylogenetic analysis of core Tillandsioideae using the nuclear...

Vriesea is the second largest genus in Tillandsioideae, the most diverse subfamily of Bromeliaceae. Although recent studies focusing on Tillandsioideae have improved the systematics of Vriesea, no consensus has been reached regarding the circumscription of the genus. Here, we present a phylogenetic analysis of core Tillandsioideae using the nuclear...

Domestication of clonally propagated crops such as pineapple from South America was hypothesized to be a ‘one-step operation’. We sequenced the genome of Ananas comosus var. bracteatus CB5 and assembled 513 Mb into 25 chromosomes with 29,412 genes. Comparison of the genomes of CB5, F153 and MD2 elucidated the genomic basis of fiber production, colo...

The tribe Geonomateae is a widely distributed group of 103 species of Neotropical palms which contains six ecologically important understory or subcanopy genera. Although it has been the focus of many studies, our understanding of the evolutionary history of this group, and in particular of the taxonomically complex genus Geonoma, is far from compl...

The adaptive radiation of Bromeliaceae (pineapple family) is one of the most diverse among Neotropical flowering plants. Diversification in this group was facilitated by several key innovations including the transition from C3 to CAM photosynthesis. We used a phylogenomic approach complemented by differential gene expression (RNA-seq) and targeted...

Understanding the genetics of biological diversification across micro‐ and macro‐evolutionary time scales is a vibrant field of research for molecular ecologists as rapid advances in sequencing technologies promise to overcome former limitations. In palms, an emblematic, economically and ecologically important plant family with high diversity in th...

Genomic imprinting is a conspicuous feature of the endosperm, a triploid tissue nurturing the embryo and synchronizing angiosperm seed development. An unknown subset of imprinted genes (IGs) is critical for successful seed development and should have highly conserved functions. Recent genome‐wide studies have found limited conservation of IGs among...

Background and aims: Defective hybrid seed development in angiosperms might mediate the rapid establishment of intrinsic post-zygotic isolation between closely related species. Extensive crosses within and among three lineages of wild tomatoes (Solanum section Lycopersicon) were performed to address the incidence, developmental timing and histolog...

Understanding the drivers and limits of species radiations is a crucial goal of evolutionary genetics and molecular ecology, yet research on this topic has been hampered by the notorious difficulty of connecting micro- and macro-evolutionary approaches to studying the drivers of diversification. To chart the current research gaps, opportunities, an...

Hybrid seed failure represents an important postzygotic barrier to interbreeding among species of wild tomatoes (Solanum section Lycopersicon) and other flowering plants. We studied genome-wide changes associated with hybrid seed abortion in the closely related Solanum peruvianum and S. chilense where hybrid crosses yield high proportions of inviab...

Inselberg-adapted species of bromeliads (Bromeliaceae) have been suggested as model systems for understanding the evolutionary genetics of species complexes and radiations in terrestrial, island-like environments. Bromeliads are particularly suitable for addressing the potential roles of interspecific gene exchange during plant speciation and radia...

Speciation often involves repeated episodes of genetic contact between divergent populations before reproductive isolation (RI) is complete. Whole genome sequencing (WGS) holds great promise for unravelling the genomic bases of speciation. We have studied two ecologically divergent, hybridizing species of the 'model tree' genus Populus (poplars, as...

Hybrid seed failure is a common reproductive barrier between plant species. For plant breeders, it represents a major obstacle to introgression of desirable traits from wild to domesticated species. Postzygotic barriers to hybridization have been well-documented among wild tomato species, and histological work showed that endosperm failure is the m...

Hybrid seed failure, a common postzygotic barrier in angiosperms, is likely mediated by abnormal endosperm development, highlighting the pivotal role of the endosperm for proper seed development. Epigenetic processes modulate the parent-of-origin specific expression of so-called “imprinted” genes in the endosperm, some of which may be important for...

Studying the divergence continuum in plants is relevant to fundamental and applied biology because of the potential to reveal functionally important genetic variation. In this context, whole-genome sequencing (WGS) provides the necessary rigour for uncovering footprints of selection. We resequenced populations of two divergent phylogeographic linea...

Rapid recent progress in ecological & evolutionary genomics is imparting fresh perspectives to the study of population divergence and speciation, i.e. the origin and maintenance of biological diversity. Our group’s research interests revolve around the use of novel laboratory and computational tools for studying adaptive evolutionary responses, spe...

Worldwide evolution of mosquito resistance to chemical insecticides represents a major challenge for public health, and the future of vector control largely relies on the development of biological insecticides that can be used in combination with chemicals (integrated management), with the expectation that populations already resistant to chemicals...

Background: Despite the intensive use of Bacillus thuringiensis israelensis (Bti) toxins for mosquito control, little is known about the long term effect of exposure to this cocktail of toxins on target mosquito populations. In contrast to the many cases of resistance to Bacillus thuringiensis Cry toxins observed in other insects, there is no evid...

Sprays of commercial preparations of the bacterium Bacillus thuringiensis subsp. israelensis are widely used for the control of mosquito larvae. Despite an abundant literature on B. thuringiensis subsp. israelensis field efficiency on mosquito control, few studies have evaluated the fate of spores in the environment after treatments. In the present...

Mosquito control is often the main method used to reduce mosquito-transmitted diseases. In order to investigate the genetic basis of resistance to the bio-insecticide Bacillus thuringiensis subsp. israelensis (Bti), we used information on polymorphism obtained from cDNA tag sequences from pooled larvae of laboratory Bti-resistant and susceptible Ae...

Effective vector control is currently challenged worldwide by the evolution of resistance to all classes of chemical insecticides in mosquitoes. In Martinique, populations of the dengue vector Aedes aegypti have been intensively treated with temephos and deltamethrin insecticides over the last fifty years, resulting in heterogeneous levels of resis...

The bacterio-insecticide Bacillus thuringiensis subsp. israelensis (Bti) represents currently a safe alternative to chemical insecticides in mosquito-borne diseases control and is intensively used worldwide. In the French Rhone-alpine mosquito Aedes rusticus Rossi, several genomic signatures of selection were detected in populations treated for mor...

Bacillus thuringiensis var. israelensis (Bti) is a natural larval mosquito pathogen producing pore-forming toxins targeting the midgut of Diptera larvae. It is used worldwide for mosquito control. Resistance mechanisms of an Aedes aegypti laboratory strain selected for 30 generations with field-collected leaf litter containing Bti toxins were inves...

All the 3512 transcripts detected by microarrays experiments in at least 5 hybridizations out of 6. For each transcript, accession number, corrected p-value, expression level changes, Vectorbase annotation and functional category are indicated.

Validation of microarray data by RT-qPCR on fifteen selected genes. Both experiments were performed on the same mRNA extracted from dissected larval midguts. ALP2, Alkaline phosphatase AAEL003298; ALP3, AAEL003313; ALP5, AAEL015070; ALP6, AAEL011175; APN1, N-Aminopeptidase AAEL012774; APN2, AAEL012776; APN3, AAEL012778; Cad2, Cadherin AAEL007488; H...

2D-DIGE gels from the two biological replicates and dye-swapping. BBMV prepared from first (A and B) and second (C and D) biological replicate are separated in function of their size (kDa) and their isoelectric point (pI). BBMV from Bti resistant strain are labeled with Cy3 and susceptible strain with Cy5 (A and C) or resistant strain with Cy5 and...

Cadherin detection by immunoblotting. BBMV proteins from the susceptible Bora-Bora strain (lane 1), LiTOX strain (lane 2) and the UGAL Aedes strain (lane 3) were separated in SDS-PAGE and stained with coomassie blue (panel A) or probed with α-AgCad1 antibodies (panel B), α-AgCad2 antibodies (panel C) or with pre-immune serum from α-AgCad2 rabbit (p...

70 transcripts significantly (corrected P-val<0.01) more than 3-fold differentially transcribed in the LiTOX strain. Transcripts are classified according to their putative function using the 13 functional categories. For each transcript, accession number, corrected P-value, expression level changes, Vectorbase annotation and supercontig are indicat...

Primer pairs used for RT-qPCR analyses. For each primer pair, sequence, corresponding gene name and accession number, product length, Tm and optimal annealing temperature used in PCR program are indicated. PCR efficiency and different parameters of the calibration curves (R2, slope and y-intercept) are also indicated. Specificity of each primer pai...

Protein identification of the 56 spots picked on deep purple stained 2D-gel. When different spots pointed to the same protein, they were differentiated using arbitrary letters after the access number. For each identification, the predicted pI, the predicted mass in kilodaltons, the percentage of sequence coverage, their functional category, and the...

Glycosylphosphatidylinositol (GPI)-anchor domains detection by four predictive computational programs. For each gene and protein, their accession number, the transcript and protein sizes are indicated. Results from the big-GPI and GPI-SOM softwares are indicated as ‘YES’ when they found a potential GPI-domain and ‘NO’ when no GPI-domain was determi...

The Amplified fragment Length Polymorphism (AFLP) is one of the cost-effective and useful fingerprinting techniques to study non-model species. One crucial AFLP step in the AFLP procedure is the choice of restriction enzymes and selective bases providing good-quality AFLP profiles. Here, we present a user-friendly program (ISIF) that allows carryin...

Genome scans based on anonymous Amplified Fragment Length Polymorphism (AFLP) markers scattered throughout the genome are becoming an increasingly popular approach to study the genetic basis of adaptation and speciation in natural populations. A shortcoming of this approach is that despite its efficiency to detect signatures of selection, it can ha...

AFLP-based genome scans are widely used to study the genetics of adaptation and to identify genomic regions potentially under selection. However, this approach usually fails to detect the actual genes or mutations targeted by selection owing to the difficulties of obtaining DNA sequences from AFLP fragments. Here, we combine classical AFLP outlier...

##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

The control of mosquitoes transmitting infectious diseases relies mainly on the use of chemical insecticides. However, resistance to most chemical insecticides threatens mosquito control programs. In this context, the spraying of toxins produced by the bacteria Bacillus thuringiensis subsp. israelensis (Bti) in larval habitats represents an alterna...

Identification of genes involved in local adaptation is particularly challenging in species functioning as a network of inter-connected populations undergoing frequent extinction-recolonisation, because populations are submitted to contrasted evolutionary pressures. Using AFLP markers, population genetic structure of the mosquito Aedes rusticus was...

Two recent high-profile studies offered empirical evidence for a “snowballing” accumulation of postzygotic incompatibilities in Drosophila and Solanum (tomatoes). Here we present a reanalysis of the Solanum data that is motivated by population genetic principles. Specifically, the high levels of intraspecific nucleotide polymorphism in wild tomato...

Sustainable insect vector disease control strategies involve delaying the evolution of resistance to insecticides in natural populations. The evolutionary dynamics of resistance in the field is highly dependent on the fitness cost of resistance alleles. To successfully manage resistance evolution in target species, it is not only important to find...

The simultaneous production of six different toxins by Bacillus thuringiensis israelensis (Bti) is thought to delay the evolution of resistance in treated mosquito populations. Recent studies have shown that Bti can persist and proliferate in the environment, thereby imposing continuous selective pressure on mosquito populations, raising concerns a...

AFLP markers are widely used in evolutionary genetics and ecology. However the frequent occurrence of non-homologous co-migrating fragments (homoplasy) both at the intra- and inter-individual levels in AFLP data sets is known to skew key parameters in population genetics. Geneticists can take advantage of the growing number of full genome sequences...

Table S1. Summary of the number of fragments and peaks per profile, homoplasy rate and maximum number of co-migrating fragments obtained in silico with all 284 different EcoRI/MseI primer combination pairs.

Table S2. Primer combinations and sample sizes used for each model/non-model species comparison and number of in silico and empirical peaks obtained.

Mosquito control represents a major public health concern, as mosquitoes transmit many severe human diseases. After the massive use of chemical insecticides since the fifties, the bacterio-insecticide Bacillus thuringiensis subsp. israelensis (Bti) represents a safe alternative and is now widely used to control mosquito populations. High toxicity d...

Identification of genes involved in local adaptation is particularly challenging for species functioning as a network of interconnected populations undergoing frequent extinctions-recolonizations, because populations are submitted to contrasted evolutionary pressures. Using amplified fragment length polymorphism markers, population genetic structur...