Sebastien Renaut

Sebastien Renaut
Université de Montréal | UdeM · Department of Biological Sciences

PhD

About

66
Publications
18,478
Reads
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3,105
Citations
Citations since 2016
22 Research Items
2016 Citations
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Introduction
My interests are in evolution, genomics, transcriptomics and ecology. More specifically, in the genomic basis of adaptation and the fundamental mechanisms underlying the origin and evolution of genome architecture. I have worked on several organisms, but mainly lake whitefish during my PhD, and wild and cultivated sunflowers during my postdoc.
Additional affiliations
September 2014 - present
Université de Montréal
Position
  • Professor
October 2010 - August 2014
University of British Columbia - Vancouver
Position
  • PostDoc Position
January 2006 - January 2010
Laval University
Position
  • PhD Student

Publications

Publications (66)
Article
Full-text available
Mutations that provide environment-dependent selective advantages drive adaptive divergence among species. Many phenotypic differences among related species are more likely to result from gene expression divergence rather than from non-synonymous mutations. In this regard, cis-regulatory mutations play an important part in generating functionally s...
Preprint
Full-text available
Mutations that provide environment dependent selective advantages drive adaptive divergence among species. Many phenotypic differences among related species are more likely to result from gene expression divergence rather than from non-synonymous mutations. In this regard, cis-regulatory mutations play an important part in generating functionally s...
Article
Full-text available
Little is known about establishment success of the arbuscular mycorrhizal fungal (AMF) inocula and their effects on a soil-indigenous community of AMF. In this study, we assessed the effect of introducing Rhizophagus irregularis DAOM-197198 in soil under field condition on the community composition of indigenous AMF in the roots of corn (Zea mays),...
Article
Full-text available
Spatial synchrony is a common characteristic of spatio‐temporal population dynamics across many taxa. While it is known that both dispersal and spatially autocorrelated environmental variation (i.e., the Moran effect) can synchronize populations, the relative contributions of each, and how they interact, is generally unknown. Distinguishing these m...
Article
Full-text available
Bivalves exhibit an astonishing diversity of sexual systems, with genetic and environmental determinants of sex, and possibly the only example of mitochondrial genes influencing sex determination pathways in animals. In contrast to all other animal species in which strict maternal inheritance (SMI) of mitochondria is the rule, bivalves possess a sy...
Article
Full-text available
Seaweeds have been used as a source of natural fertilizer and biostimulant in agriculture for centuries. However, their effects on soil and crop root microbiota remain unclear. Here, we used a commercially available Ascophyllum nodosum extract (ANE) to test its effect on bacterial and fungal communities of rhizospheric soils and roots of pepper and...
Article
Full-text available
Freshwater mussels (Bivalvia: Unionida) serve an important role as aquatic ecosystem engineers but are one of the most critically imperilled groups of animals. Here, we used a combination of sequencing strategies to assemble and annotate a draft genome of Venustaconcha ellipsiformis, which will serve as a valuable genomic resource given the ecologi...
Article
Full-text available
Data are one of the primary outputs of science. Although certain subdisciplines of biology have pioneered efforts to ensure their long-term preservation and facilitate collaborations, data continue to disappear, owing mostly to technological, regulatory, and ideological hurdles. In this article, we describe the important steps toward proper data ma...
Article
Full-text available
Bivalves exhibit an astonishing diversity of sexual systems and sex-determining mechanisms. They can be gonochoric, hermaphroditic or androgenetic, with both genetic and environmental factors known to determine or influence sex. One unique sex-determining system involving the mitochondrial genome has also been hypothesized to exist in bivalves with...
Article
Full-text available
Peer review of research articles is a core part of our scholarly communication system. In spite of its importance, the status and purpose of peer review is often contested. What is its role in our modern digital research and communications infrastructure? Does it perform to the high standards with which it is generally regarded? Studies of peer rev...
Article
The Athabasca oil sand deposit is one of the largest single oil deposits in the world. Following surface mining, companies are required to restore soil-like profiles that can support the previous land capabilities. The objective of this study was to assess whether the soil prokaryotic alpha diversity (α-diversity) and β-diversity in oil sand soils...
Article
Aims Habitat connectivity is important in conservation since isolation can diminish the potential of a population for adaptation and increase its risk of extinction. However, conservation of naturally patchy ecosystems such as peatlands has mainly focused on preserving specific sites with exceptional characteristics, neglecting the potential interc...
Article
Full-text available
Mountain ash ( Sorbus decora and S. americana ) is used by the Cree Nation of the James Bay region of Quebec (Eeyou Istchee) as traditional medicine. Its potential as an antidiabetic medicine is thought to vary across its geographical range, yet little is known about the factors that affect its antioxidant capacity. Here, we examined metabolite gen...
Article
Full-text available
Aims Habitat connectivity is important in conservation since isolation can diminish the potential of a population for adaptation and increase its risk of extinction. However, conservation of naturally patchy ecosystems such as peatlands has mainly focused on preserving specific sites with exceptional characteristics, neglecting the potential interc...
Article
Full-text available
Size-selective harvest may lead to over-exploitation of commercial fisheries, but the population genetic and evolutionary consequences of such practices remain poorly understood. We investigated the role of within-generation selection in a historically over-exploited Lake Whitefish (Coregonus clupeaformis) population associated with fisheries-induc...
Article
Press stop, erase everything from now till some arbitrary time in the past and start recording life as it evolves once again. Would you see the same tape of life playing itself over and over, or would a different story unfold every time? The late Steven Jay Gould called this experiment replaying the tape of life and argued that any replay of the ta...
Article
Full-text available
Data are the foundation of empirical research, yet all too often the datasets underlying published papers are unavailable, incorrect, or poorly curated. This is a serious issue, because future researchers are then unable to validate published results or reuse data to explore new ideas and hypotheses. Even if data files are securely stored and acces...
Article
For populations to maintain optimal fitness, harmful mutations must be efficiently purged from the genome. Yet, under circumstances that diminish the effectiveness of natural selection, such as the process of plant and animal domestication, deleterious mutations are predicted to accumulate. Here, we compared the load of deleterious mutations in 21...
Preprint
Full-text available
Data are the foundation of empirical research, yet all too often the datasets underlying published papers are unavailable, incorrect, or poorly curated. This is a serious issue, because future researchers are then unable to validate published results or reuse data to explore new ideas and hypotheses. While data files may be securely stored and acce...
Preprint
Full-text available
Data are the foundation of empirical research, yet all too often the datasets underlying published papers are unavailable, incorrect, or poorly curated. This is a serious issue, because future researchers are then unable to validate published results or reuse data to explore new ideas and hypotheses. While data files may be securely stored and acce...
Data
These are the contigs assembled in the context of the RNA-seq experiment performed in Dion-Cote et al. 2014 Molecular Biology and Evolution.
Article
Hybridization is thought to play an important role in plant evolution by introducing novel genetic combinations and promoting genome restructuring. However, surprisingly little is known about the impact of hybridization on transposable element (TE) proliferation and the genomic response to TE activity. In this paper, we first review the mechanisms...
Article
Full-text available
Knowledge of the nature and extent of karyotypic differences between species provides insight into the evolutionary history of the genomes in question and, in the case of closely related species, the potential for genetic exchange between taxa. We constructed high-density genetic maps of the silverleaf sunflower (Helianthus argophyllus) and Algodon...
Article
Identifying the molecular basis of reproductive isolation among diverging lineages represents an essential step towards understanding speciation in natural populations. Post-zygotic barriers can lead to hybrid breakdown, a syndrome that has been documented in several systems, potentially involving the reactivation of transposable elements. In north...
Article
Policies ensuring that research data are available on public archives are increasingly being implemented at the government [1], funding agency [2-4], and journal [5, 6] level. These policies are predicated on the idea that authors are poor stewards of their data, particularly over the long term [7], and indeed many studies have found that authors a...
Article
The role of natural selection in promoting reproductive isolation has received substantial renewed interest within the last two decades. As a consequence, the study of ecological speciation has become an extremely productive research area in modern evolutionary biology. Recent innovations in sequencing technologies offer an unprecedented opportunit...
Article
The repeated evolution of traits in organisms facing similar environmental conditions is considered to be fundamental evidence for the role of natural selection in moulding phenotypes. Yet, aside from case studies of parallel evolution and its genetic basis, the repeatability of evolution at the level of the whole genome remains poorly characterize...
Article
Latest technological developments in evolutionary biology bring new challenges in documenting the intricate genetic architecture of species in the process of divergence. Sympatric populations of lake whitefish represent one of the key systems to investigate this issue. Despite the value of random genotype-by-sequencing methods and decreasing cost o...
Article
This article documents the public availability of three transcriptome sequences. These genomic resources were developed for the following species: Helianthus anomalus, Helianthus deserticola and Helianthus paradoxus.
Article
Full-text available
Genomic studies of speciation often report the presence of highly differentiated genomic regions interspersed within a milieu of weakly diverged loci. The formation of these speciation islands is generally attributed to reduced inter-population gene flow near loci under divergent selection, but few studies have critically evaluated this hypothesis....
Article
Variation in patterns of gene expression contributes to phenotypic diversity and can ultimately predict adaptive responses. However, in many cases, the consequences of regulatory mutations on patterns of gene expression and ultimately phenotypic differences remain elusive. A standard way to study the genetic architecture of expression variation in...
Article
Full-text available
The data underlying scientific papers should be accessible to researchers both now and in the future, but how best can we ensure that these data are available? Here we examine the effectiveness of four approaches to data archiving: no stated archiving policy, recommending (but not requiring) archiving, and two versions of mandating data deposition...
Article
Genomic studies of speciation often report the presence of highly differentiated genomic regions interspersed within a milieu of weakly diverged loci. The formation of these speciation islands is generally attributed to reduced inter-population gene flow near loci ...
Article
Full-text available
Few studies have investigated the causes of evolutionary rate variation among plant nuclear genes, especially in recently diverged species still capable of hybridizing in the wild. The recent advent of Next Generation Sequencing (NGS) permits investigation of genome wide rates of protein evolution and the role of selection in generating and maintai...
Article
Full-text available
Abstract Reproducibility is the benchmark for results and conclusions drawn from scientific studies, but systematic studies on the reproducibility of scientific results are surprisingly rare. Moreover, many modern statistical methods make use of 'random walk'model fitting procedures, and these are inherently stochastic in their output. Does the...
Article
Full-text available
The nature, size and distribution of the genomic regions underlying divergence and promoting repro- ductive isolation remain largely unknown. Here, we summarize ongoing efforts using young (12 000 yr BP) species pairs of lake whitefish (Coregonus clupeaformis) to expand our understanding of the initial genomic patterns of divergence observed during...
Article
The first North American RAD Sequencing and Genomics Symposium, sponsored by Floragenex (http://www.floragenex.com/radmeeting/), took place in Portland, Oregon (USA) on 19 April 2011. This symposium was convened to promote and discuss the use of restriction-site-associated DNA (RAD) sequencing technologies. RAD sequencing is one of several strategi...
Article
Natural hybridization between closely related taxa is frequent in many organismal groups, yet it has long been perceived as a force preventing diversification and speciation, especially so in animals. In recent years, growing evidence in favour of hybridization facilitating adaptive divergence has accumulated (Mallet 2007; Mavárez & Linares 2008; N...
Article
Full-text available
Identifying DNA regions evolving under the effect of either positive or stabilizing selection, and quantifying the intensity of the selective pressures at play, represent major goals in evolutionary biology. The combination of next generation sequencing with a comparative genomics approach appears particularly promising towards yielding detailed in...
Article
As populations adapt to novel environments, divergent selection will promote heterogeneous genomic differentiation via reductions in gene flow for loci underlying adaptive traits. Using a data set of over 100 SNP markers, genome scans were performed to investigate the effect of natural selection maintaining differentiation in five lakes harbouring...
Article
Full-text available
Genetic analyses of speciation have focused nearly exclusively on retrospective analyses of reproductive isolation between highly divergent species. Yet, a full understanding of the speciation process must encompass analysis of the consequences of genomic divergence in young lineages still capable of exchanging genes under natural conditions. The a...
Article
Gene expression divergence is one of the mechanisms thought to be involved in the emergence of incipient species. Next-generation sequencing has become an extremely valuable tool for the study of this process by allowing whole transcriptome sequencing, or RNA-Seq. We have conducted a 454 GS-FLX pyrosequencing experiment to refine our understanding...
Article
Full-text available
In contrast to the large amount of ecological information supporting the role of natural selection as a main cause of population divergence and speciation, an understanding of the genomic basis underlying those processes is in its infancy. In this paper, we review the main findings of a long-term research programme that we have been conducting on t...
Article
Next-generation sequencing allows the discovery of large numbers of single nucleotide polymorphisms (SNPs) in species where little genomic information was previously available. Here, we assembled, de novo, over 130 mb of non-normalized cDNA using 454 pyrosequencing data from dwarf and normal lake whitefish and backcross hybrids. Our main goals were...
Data
Regulatory changes between juvenile dwarf and normal whitefish at candidate adaptive traits. Comparison of significant regulatory changes between juvenile dwarf and normal whitefish with patterns observed at candidate adaptive traits. Derome et al. [20] and St-Cyr et al. [22] analysed gene expression in white muscle and liver tissue of adult fish f...
Data
EST clones for which significant divergence was detected between embryos or juveniles of dwarf and normal whitefish. List of all EST clones for which significant divergence of gene expression was detected for dwarf and normal whitefish (33 and 502 EST clones for the Embryo and Juvenile datasets). EST clone and annotation, the Log2-fold change of dw...
Data
Regulatory changes between juvenile dwarf and normal whitefish in a common environment. Similarity of regulatory changes between dwarf and normal whitefish at different life history stages in controlled common environments. All comparisons are based on the same strains (Lake Témiscouata "dwarf" and Lake Aylmer "normal" respectively). 108 EST clones...
Article
Full-text available
Genomewide analyses of the transcriptome have confirmed that gene misexpression may underlie reproductive isolation mechanisms in interspecific hybrids. Here, using a 16,006 features cDNA microarray, we compared and contrasted gene expression divergence at two ontogenetic stages in incipient species of normal and dwarf whitefish (Coregonus clupeafo...
Article
Full-text available
The evolution of barriers to reproduction is of key interest to understand speciation. However, there may be a current bias towards studying intrinsic postzygotic isolation in old species pairs as compared to the emergence of barriers to gene flow through adaptive divergence. This study evaluates the relative importance of both processes in the evo...
Article
Full-text available
A method to significantly improve the germination and development of plantlets of Aplectrum hyemale was developed. Seeds of this terrestrial orchid were collected in a natural stand, surface disinfected and grown in vitro on a gellified growth medium in absence of symbiotic fungi. Seeds were sowed whole or after excision of the seed coat. Embryos t...
Article
Full-text available
We used microarrays and a previously established linkage map to localize the genetic determinants of brain gene expression for a backcross family of lake whitefish species pairs (Coregonus sp.). Our goals were to elucidate the genomic distribution and sex specificity of brain expression QTL (eQTL) and to determine the extent to which genes controll...
Article
We measured the mean fitness of populations of Chlamydomonas reinhardtii maintained in the laboratory as obligately sexual or asexual populations for about 100 sexual cycles and about 1000 asexual generations. Sexuality (random gamete fusion followed by meiosis) is expected to reduce mutational load and increase mean fitness by combining deleteriou...
Conference Paper
The late Stephen Gould argued that “rewinding the tape of life” would produce a very different array of end products, but others have reported that the evolution of some traits and species can be surprisingly repeatable. However, little is known about the repeatability of evolution at the genomic level. Here we employ transcriptome sequences from t...
Conference Paper
The world is likely to experience a series of increasingly severe food crises over the next century. While these episodes will no doubt have many underlying causes, there is a general consensus about the need to maximize crop productivity, while minimizing resource use and environmental damage. An especially promising approach, in our view, is the...