François Hébert

Targeted sequence capture and resequencing implies a predominant role of regulatory regions in the divergence of a sympatric lake whitefish species pair (Coregonus clupeaformis)

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 of sequencing technologies, it remains challenging to investigate variation in coding regions, especially in the case of recently duplicated genomes as in salmonids, as this greatly complicates whole genome resequencing. We thus designed a sequence capture array targeting 2773 annotated genes to document the nature and the extent of genomic divergence between sympatric dwarf and normal whitefish. Among the 2728 genes successfully captured, a total of 2182 coding and 10 415 noncoding putative single‐nucleotide polymorphisms (SNPs) were identified after applying a first set of basic filters. A genome scan with a quality‐refined selection of 2203 SNPs identified 267 outlier SNPs in 210 candidate genes located in genomic regions potentially involved in whitefish divergence and reproductive isolation. We found highly heterogeneous FST estimates among SNP loci. There was an overall low level of coding polymorphism, with a predominance of noncoding mutations among outliers. The heterogeneous patterns of divergence among loci confirm the porous nature of genomes during speciation with gene flow. Considering that few protein‐coding mutations were identified as highly divergent, our results, along with previous transcriptomic studies, imply that changes in regulatory regions most likely had a greater role in the process of whitefish population divergence than protein‐coding mutations. This study is the first to demonstrate the efficiency of large‐scale targeted resequencing for a nonmodel species with such a large and unsequenced genome.

Nonparallelism in MHCIIβ diversity accompanies nonparallelism in pathogen infection of lake whitefish (Coregonus clupeaformis) species pairs as revealed by next-generation sequencing.

Major histocompatibility (MHC) immune system genes may evolve in response to pathogens in the environment. Because they also may affect mate choice, they are candidates for having great importance in ecological speciation. Here, we use next‐generation sequencing to test the general hypothesis of parallelism in patterns of MHCIIβ diversity and bacterial infections among five dwarf and normal whitefish sympatric pairs. A second objective was to assess the functional relationships between specific MHCIIβ alleles and pathogens in natural conditions. Each individual had between one and four alleles, indicating two paralogous loci. In Cliff Lake, the dwarf ecotype was monomorphic for the most common allele. In Webster Lake, the skew in the allelic distribution was towards the same allele but in the normal ecotype, underscoring the nonparallel divergence among lakes. Our signal of balancing selection matched putative peptide binding region residues in some cases, but not in others, supporting other recent findings of substantial functional differences in fish MHCIIβ compared with mammals. Individuals with fewer alleles were less likely to be infected; thus, we found no evidence for the heterozygote advantage hypothesis. MHCIIβ alleles and pathogenic bacteria formed distinct clusters in multivariate analyses, and clusters of certain alleles were associated with clusters of pathogens, or sometimes the absence of pathogens, indicating functional relationships at the individual level. Given that patterns of MHCIIβ and bacteria were nonparallel among dwarf and normal whitefish pairs, we conclude that pathogens driving MHCIIβ evolution did not play a direct role in their parallel phenotypic evolution.

The Biology of Canadian Weeds. 146. Rhododendron groenlandicum (Oeder) Kron and Judd

Hébert, F. and Thiffault, N. 2011. The Biology of Canadian Weeds. 146. Rhododendron groenlandicum (Oeder) Kron and Judd. Can. J. Plant Sci. 91: 725-738. Rhododendron groenlandicum (Oeder) Kron and Judd, bog Labrador tea, is an evergreen shrub from the Ericacae family native to North America. Bog Labrador tea is associated with the later stages of forest successions in black spruce forest stands of the boreal ecosystems with cool climates, but responds aggressively to forest openings where it is already present. In general, bog Labrador tea is associated with nutrient-poor, acidic soils, with drainage ranging from moist to wet. Layering is the main regeneration strategy of the species; evidence suggests that this could be especially true following disturbances that open the forest canopy. Sexual reproduction maintains viability in undisturbed communities through wind or water dispersal. Rhododendron groenlandicum acclimates more rapidly relative to black spruce after perturbations through a higher rate of resource utilization when resources are available. The species is a highly competitive shrub for soil nutrients; it competes with regenerating conifers for soil nitrogen and phosphorus. It can also assimilate organic nitrogen from the soil through its mycorhizae. These characteristics may lead to the formation of ericaceous heaths that can stay unforested indefinitely. However, this species can be eradicated by herbicides (glyphosate) and heavy site scarification can limit its propagation.

Major host transitions are modulated through transcriptome-wide reprogramming events inSchistocephalus solidus, a threespine stickleback parasite

Parasites with complex life cycles have developed numerous phenotypic strategies, closely associated with developmental events, to enable the exploitation of different ecological niches and facilitate transmission between hosts. How these environmental shifts are regulated from a metabolic and physiological standpoint, however, still remain to be fully elucidated. We examined the transcriptomic response of Schistocephalus solidus, a trophically transmitted parasite with a complex life cycle, over the course of its development in an intermediate host, the threespine stickleback, and the final avian host. Results from our differential gene expression analysis show major reprogramming events among developmental stages. The final host stage is characterized by a strong activation of reproductive pathways and redox homoeostasis. The attainment of infectivity in the fish intermediate host—which precedes sexual maturation in the final host and is associated with host behaviour changes—is marked by transcription of genes involved in neural pathways and sensory perception. Our results suggest that un‐annotated and S. solidus‐specific genes could play a determinant role in host–parasite molecular interactions required to complete the parasites life cycle. Our results permit future comparative analyses to help disentangle species‐specific patterns of infection from conserved mechanisms, ultimately leading to a better understanding of the molecular control and evolution of complex life cycles.

Can the behaviour of threespine stickleback parasitized with Schistocephalus solidus be replicated by manipulating host physiology

ABSTRACT Sticklebacks infected by the parasitic flatworm Schistocephalus solidus show dramatic changes in phenotype, including a loss of species-typical behavioural responses to predators. The timing of host behaviour change coincides with the development of infectivity of the parasite to the final host (a piscivorous bird), making it an ideal model for studying the mechanisms of infection-induced behavioural modification. However, whether the loss of host anti-predator behaviour results from direct manipulation by the parasite, or is a by-product (e.g. host immune response) or side effect of infection (e.g. energetic loss), remains controversial. To understand the physiological mechanisms that generate these behavioural changes, we quantified the behavioural profiles of experimentally infected fish and attempted to replicate these in non-parasitized fish by exposing them to treatments including immunity activation and fasting, or by pharmacologically inhibiting the stress axis. All fish were screened for the following behaviours: activity, water depth preference, sociability, phototaxis, anti-predator response and latency to feed. We were able to change individual behaviours with certain treatments. Our results suggest that the impact of S. solidus on the stickleback might be of a multifactorial nature. The behaviour changes observed in infected fish might result from the combined effects of modifying the serotonergic axis, lack of energy and activation of the immune system. Summary: Hypotheses regarding causes of the behavioural modifications in threespine stickleback parasitized with the flatworm Schistocephalus solidus are tested by analyzing behaviour changes induced by experimental manipulations.

Identification of candidate mimicry proteins involved in parasite-driven phenotypic changes

BackgroundEndoparasites with complex life cycles are faced with several biological challenges, as they need to occupy various ecological niches throughout their development. Host phenotypes that increase the parasite’s transmission rate to the next host have been extensively described, but few mechanistic explanations have been proposed to describe their proximate causes. In this study we explore the possibility that host phenotypic changes are triggered by the production of mimicry proteins from the parasite by using an ecological model system consisting of the infection of the threespine stickleback (Gasterosteus aculeatus) by the cestode Schistocephalus solidus.MethodUsing RNA-seq data, we assembled 9,093 protein-coding genes from which ORFs were predicted to generate a reference proteome. Based on a previously published method, we built two complementary analysis pipelines to i) establish a general classification of protein similarity among various species (pipeline A) and ii) identify candidate mimicry proteins showing specific host-parasite similarities (pipeline B), a key feature underlying the possibility of molecular mimicry.ResultsNinety-four tapeworm proteins showed high local sequence homology with stickleback proteins. Four of these candidates correspond to secreted or membrane proteins that could be produced by the parasite and eventually be released in or be in contact with the host to modulate physiological pathways involved in various phenotypes (e.g. behaviors). One of these candidates belongs to the Wnt family, a large group of signaling molecules involved in cell-to-cell interactions and various developmental pathways. The three other candidates are involved in ion transport and post-translational protein modifications. We further confirmed that these four candidates are expressed in three different developmental stages of the cestode by RT-PCR, including the stages found in the host.ConclusionIn this study, we identified mimicry candidate peptides from a behavior-altering cestode showing specific sequence similarity with host proteins. Despite their potential role in modulating host pathways that could lead to parasite-induced phenotypic changes and despite our confirmation that they are expressed in the developmental stage corresponding to the altered host behavior, further investigations will be needed to confirm their mechanistic role in the molecular cross-talk taking place between S. solidus and the threespine stickleback.

Does Trait Plasticity of Three Boreal Nutrient-Conserving Species Relate to their Competitive Ability?

Abstract: The present study investigates potential differences in trait plasticity as an additional contributing mechanism explaining ericaceous shrub dominance during different periods after logging. Two ericaceous species (Kalmia angustifolia, Rhododendron groenlandicum), and black spruce plants (Picea mariana), were submitted to combinations of 3 light levels and 2 levels of nitrogen addition during a simulated growing season of 9 weeks under greenhouse conditions. Plant traits related to light (photosynthesis, leaf mass per unit of area, leaf and aboveground biomass allocation, foliar N concentration) and nutrient acquisition (root mass ratio, specific absorption ratio, absorption of 15N) were measured in response to the manipulation of these resources. The leaf mass per unit of area (LMA) of both ericaceous species was significantly reduced by shading; LMA of Rhododendron and Kalmia was, respectively, 54% and 31% higher in the highest light treatment. The LMA of black spruce was unchanged in response to light level. There were few differences among species in trait response to N addition. Black spruce was characterized by higher nutrient absorption rate and specific absorption rate at higher N levels compared to the 2 ericads. With the exception of LMA, plasticity to light was higher for Kalmia; in contrast, plasticity to N addition was higher for Rhododendron and black spruce. Finally, LMA appears to be a key trait explaining the competitive advantage of ericaceous species (especially Rhododendron) and potential encroachment on forested sites after disturbance.

Field Photosynthesis Measurements on Black Spruce (Picea mariana): Does Needle Age Matter?

Black spruce (Picea mariana) trees have needles that persist for a number of years, and it is not clear which age class should be evaluated for photosynthesis to best understand physiological responses. Moreover, the impact of sampling current versus older foliage is rarely acknowledged in published literature, even though it may influence the interpretation of results. We compared the photosynthesis rate of current and 1-year-old foliage of black spruce natural regeneration during three growing seasons. The photosynthesis rate was consistently greater for 1-year-old needles compared to current-year needles at the beginning of each growing season; however, after about 1 month, rates were similar between the two age classes. This same pattern was repeated every season and was independent of light availability induced by different harvesting treatments. We suggest that photosynthesis measurements of black spruce should be performed on 1-year-old needles instead of current-year foliage to ensure more uniform photosynthesis values throughout the season.

Recovery of plant community functional traits following severe soil perturbation in plantations: a case-study

ABSTRACT We present a case study in which we assessed the effects of a severe soil perturbation on the plant community and soil variables in young hybrid poplar (Populus sp.) plantations of southern Québec (Canada). Our overall goal was to test if soil perturbation and planting fast-growing species could promote the reestablishment of a relatively diverse plant community. A chronosequence that included three plantations (4, 8, and 12-year old) established after soil scarification, paired with three natural stands representative of the local temperate mixedwood forest comprising both pioneer and late-successional tree species, was implemented. Vegetation surveys and soil collection were performed in 2012 and species traits were provided by the Traits Of Plants In Canada and TRY databases. Principal response curve analyses showed species and functional trait divergence between treated and natural stands at ages 4 and 8, but that those divergences were less at age 12. Species and trait convergences were slower in the scarification furrows than in the scarification berms (mounds between furrows). However, severe site preparation did not appear to affect soil variables on the study sites. Our results suggest that even following severe site preparation, gradual recovery of species and trait composition similar to that of natural stands appears possible in the long term, mainly through fast canopy development by hybrid poplar. However, organic material export and soil erosion risks associated with this type of site preparation need to be evaluated. EDITED BY Sheila Ward

Divergent brain gene expression profiles between alternative behavioural helper types in a cooperative breeder

Juveniles of the cooperatively breeding cichlid fish Neolamprologus pulcher either consistently provide help in form of alloparental egg care (“cleaners”) or consistently abstain from helping (“noncleaners”). These phenotypes are not based on heritable genetic differences. Instead, they arise during ontogeny, which should lead to differences in brain structure or physiology, a currently untested prediction. We compared brain gene expression profiles of cleaners and noncleaners in two experimental conditions, a helping opportunity and a control condition. We aimed to identify (a) expression differences between cleaners and noncleaners in the control, (b) changes in gene expression induced by the opportunity and (c) differences in plasticity of gene expression between cleaners and noncleaners. Control cleaners and noncleaners differed in the expression of a single gene, irx2, which regulates neural differentiation. During the opportunity, cleaners and noncleaners had three upregulated genes in common, which were implicated in neuroplasticity, hormonal signalling and cell proliferation. Thus, the stimulus in the opportunity was sufficiently salient. Cleaners also showed higher expression of seven additional genes that were unique to the opportunity. One of these cleaner‐specific genes is implicated in neuropeptide metabolism, indicating that this process is associated with cleaning performance. This suggests that the two types employed different pathways to integrate social information, preparing them for accelerated reaction to future opportunities. Interestingly, three developmental genes were downregulated between the control and the opportunity in cleaners only. Our results indicate that the two behavioural types responded differently to the helping opportunity and that only cleaners responded by downregulating developmental genes.