Browsing by Author "Poissant, Jocelyn"

Now showing 1 - 12 of 12
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    A database for ITS2 sequences from nematodes
    (2020-07-10) Workentine, Matthew L; Chen, Rebecca; Zhu, Shawna; Gavriliuc, Stefan; Shaw, Nicolette; Rijke, Jill d; Redman, Elizabeth M; Avramenko, Russell W; Wit, Janneke; Poissant, Jocelyn; Gilleard, John S
    Abstract Background Marker gene surveys have a wide variety of applications in species identification, population genetics, and molecular epidemiology. As these methods expand to new types of organisms and additional markers beyond 16S and 18S rRNA genes, comprehensive databases are a critical requirement for proper analysis of these data. Results Here we present an ITS2 rDNA database for marker gene surveys of both free-living and parasitic nematode populations and the software used to build the database. This is currently the most complete and up-to-date ITS2 database for nematodes and is able to reproduce previous analysis that used a smaller database. Conclusions This database is an important resource for researchers working on nematodes and also provides a tool to create ITS2 databases for any given taxonomy.
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    An Assessment of Caribou (Rangifer tarandus) Genomic Diversity and Structure in Western Canada to Guide Species Conservation and Management
    (2023-01-26) Michalak, Anita; Poissant, Jocelyn; Musiani, Marco; Polfus, Jean; Rogers, Sean
    Human-induced environmental change is one of the biggest threats to global biological diversity, and the resulting environmental conditions have made it increasingly difficult for species to adapt and survive. The use of genomic technologies, such as the inference of genetic structure, can aid species conservation and prevent population declines. Particularly for caribou (Rangifer tarandus), which are considered an at-risk species across Canada, determining population genetic structure can help delineate units for conservation while detecting potentially cryptic population structure and diversity as well as undetected and/or mislabeled populations. For my M.Sc. thesis, I studied genomic diversity in caribou sampled throughout western Canada to better characterize population structure and supplement previous genetic studies conducted in this region. I accomplished this using several population structure inference methods and by combining individual-based genomic and spatial data for 658 individuals derived from 41 herds across British Columbia (BC) and Alberta (AB). Results indicate that population structure inferred from genomic data reflects neither past nor present caribou classification schemes. Instead, caribou genetic differentiation in BC and AB is best reflected at K=4 clusters, which primarily: (1) identifies a potential new conservation unit composed of individuals belonging to Itcha-Ilgachuz and neighboring subpopulations, and (2) redefines the boundaries of existing populations. Despite the need for multiple lines of evidence to provide complementary criteria for designating distinct units for conservation or populations, my work illustrates how genomics can help inform and improve the delineation of such conservation and management units for caribou.
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    Bacterial and parasitic microbiome of mantled howler monkeys: interactions and implications of human disturbance
    (2021-04-28) Macfarland, Colin Evan; Melin, Amanda; Buret, Andre G.; Kutz, Susan J.; Wasmuth, James; Pavelka, Mary Susan; Poissant, Jocelyn; Peric, Sabrina
    The gastrointestinal (GI) microbiome plays a significant role in contributing to the digestive health of the host. The community of bacteria, parasites and other microorganisms that make up the GI microbiome are known to change in response to external and internal factors including diet, stress, infection, and other environmental conditions. GI parasites are typically harmful organisms that affect hosts through triggering inflammatory response, reducing nutrient availability, and change mutualistic bacterial communities in the gut. However, they have been found to benefit the host in some circumstances. For example, helminthic parasites may have a role protecting the host from chronic inflammation caused by pathogenic bacteria or inflammatory bowel disease. In this thesis, I study the gut bacteria and parasites of populations of mantled howler monkeys (Alouatta palliata) in northwestern Costa Rica. I examine the extent to which the bacterial microbiome of howler monkeys is different in the presence of infection by helminths, and if howlers living in areas of anthropogenic habitat fragmentation have observable differences in the bacterial microbiome or helminth parasites. I used coprological examination of fecal flotations to assess parasitism, and 16S high-throughput sequencing to assess bacterial abundances. I found evidence of several helminth taxa infecting these howlers, including from the genera Controrchis, Strongyloides, Enterobius, and an unidentified Trematode. Howler monkeys infected with helminth parasites did not show a significantly different bacterial diversity; however, helminth-positive howlers have significant differences in relative abundances of Clostridiales and Bacteroidales bacteria. Furthermore, I found that howlers living in areas with anthropogenic habitat fragmentation had significantly lower diversity of gastrointestinal bacteria than howlers living in continuous forest. Lastly, I found that the howler populations within Sector Santa Rosa had a higher density of parasite infection, compared to those living in anthropogenically fragmented habitats. My research on the gastrointestinal and parasite microbiome of howlers provides new insights into the health and ecology of wild primates; further research that compares phenomena occurring in human populations and non-human primates is likely to be fruitful. My work provides new data on the impacts of habitat fragmentation that can inform primate conservation efforts, health monitoring efforts, and management decisions.
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    Both candidate gene and neutral genetic diversity correlate with parasite resistance in female Mediterranean mouflon
    (2019-03-05) Portanier, Elodie; Garel, Mathieu; Devillard, Sébastien; Maillard, Daniel; Poissant, Jocelyn; Galan, Maxime; Benabed, Slimania; Poirel, Marie-Thérèse; Duhayer, Jeanne; Itty, Christian; Bourgoin, Gilles
    Abstract Background Parasite infections can have substantial impacts on population dynamics and are accordingly a key challenge for wild population management. Here we studied genetic mechanisms driving parasite resistance in a large herbivore through a comprehensive approach combining measurements of neutral (16 microsatellites) and adaptive (MHC DRB1 exon 2) genetic diversity and two types of gastrointestinal parasites (nematodes and coccidia). Results While accounting for other extrinsic and intrinsic predictors known to impact parasite load, we show that both neutral genetic diversity and DRB1 are associated with resistance to gastrointestinal nematodes. Intermediate levels of multi-locus heterozygosity maximized nematodes resistance, suggesting that both in- and outbreeding depression might occur in the population. DRB1 heterozygosity and specific alleles effects were detected, suggesting the occurrence of heterozygote advantage, rare-allele effects and/or fluctuating selection. On the contrary, no association was detected between genetic diversity and resistance to coccidia, indicating that different parasite classes are impacted by different genetic drivers. Conclusions This study provides important insights for large herbivores and wild sheep pathogen management, and in particular suggests that factors likely to impact genetic diversity and allelic frequencies, including global changes, are also expected to impact parasite resistance.
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    Characterizing the gastrointestinal microbiome of endangered greater sage-grouse (Centrocercus urophasianus) in a conservation program
    (2023-01-18) Vaasjo, Emma; Whiteside, Douglas; Black, Sandra; Poissant, Jocelyn
    Greater sage-grouse (Centrocercus urophasianus) are a critically endangered species in Canada with fewer than 140 individuals remaining on native habitats in southern Alberta and Saskatchewan. The Wilder Institute/Calgary Zoo has initiated North America’s only zoo-based conservation breeding program for this species to bolster declining wild populations through conservation reintroductions. The biodiversity of host-associated microbiota is increasingly recognized as a component of wildlife conservation as studies demonstrate the relationship of the microbiome with growth and development, digestion, toxin metabolism, and immune function. Though the importance of microbiome research is becoming more widely known, there is considerably less literature on free-ranging, captive, or domestic avian species compared to mammalian species. Within the managed population of sage-grouse, the largest proportion of morbidity and mortality have been associated with intestinal bacterial infections. Hypothesizing that a lack of bacterial diversity or an altered bacterial community composition may have health effects on the population in both managed care and post-release, the fecal microbiome of adult and juvenile captive sage-grouse was characterized with 16s rRNA sequencing and compared to samples from wild birds. Antibiotic use and sex did not have a significant impact on the diversity or composition of the microbiome in zoo-based animals, but management of juvenile sage-grouse did influence the development of the microbiome. Juveniles that were raised outdoors with access to maternal care developed a microbiome much more similar to captive adults when compared to chicks that were incubated and hand-raised. Significant differences were noted between the captive and wild microbiome when comparing wild samples to both captive adults, and the oldest juveniles temporarily housed in soft-release pens. Differences were driven primarily by altered community composition, and not by a lack of diversity in the managed population. The local environment and diet appear to be important factors influencing the diversity and composition of the gastrointestinal microbiome in this species. Other variables related to captivity, including proximity to humans and chronic stress, may also be contributing to the significant difference seen between managed and wild populations of endangered greater sage-grouse, and deserve further exploration.
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    Developing long-read Oxford Nanopore nemabiome metabarcoding for ovine gastrointestinal nematode community analysis and diagnostics
    (2024-02-02) Charrier, Eleonore; Gilleard, John; Wasmuth, James; Poissant, Jocelyn; Levy, Michel; McVeigh, Paul; Summers, Mindi
    Parasitic gastrointestinal nematodes (GIN) are major causes of disease in animals and humans and the routine use of anthelmintic drugs in their management is increasingly ineffective due to widespread anthelmintic drug resistance. Consequently, there is a growing need for improved diagnostic tools to enable more evidence-based approaches to control including more targeted and sustainable drug use. ITS-2 nemabiome metabarcoding is a powerful method to determine the relative abundance of GIN species isolated from fecal samples from a number of animal species. This thesis presents research aiming to improve this method to increase its flexibility, widen its applicability and make it more suitable for more routine diagnostics and surveillance. Sheep are an excellent system to develop GIN molecular diagnostic methods; GIN are arguably better studied in sheep than in any other host due to their major impact on sheep production. The research in this thesis has three main aims: (i) To transition nemabiome metabarcoding away from the short-read Illumina platform to the long-read Oxford Nanopore Technologies (ONT) platform. (ii) To apply nemabiome metabarcoding directly to DNA from fecal material rather than harvested parasite populations. (iii) To develop nemabiome metabarcoding to determine the absolute abundance of GIN in fecal samples rather than just their relative abundance. Chapter 2 presents a set of four new non-redundant nematode rRNA databases and a WebApp, ‘PrimerTC’, to assess the taxonomic conservation of primers targeting different regions of the rRNA cistron across the nematode phylum. These new resources should enable more targeted and more comprehensive metabarcoding for both parasitic and free-living nematodes. Chapter 3 introduces ITS-1/5.8S/ITS-2 rRNA long-read ONT metabarcoding for GIN species relative quantitation. This chapter also pioneers the application of ITS-2 and ITS-1/5.8S/ITS-2 metabarcoding directly to DNA extracted from ovine fecal samples. Chapter 4 explores a synthetic DNA spike-in approach for absolute quantitation of GIN species in ovine fecal samples using both ITS-2 rDNA Illumina short-read and ITS-1/5.8S/ITS-2 long-read nemabiome metabarcoding. The new tools and methodologies presented in this thesis should pave the way for more widescale adoption of nemabiome metabarcoding as a tool in research, surveillance, and routine diagnostics.
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    Development of non-invasive genomic tools for feral horses
    (2023-01-24) Gavriliuc, Stefan Teodor; Poissant, Jocelyn; Wasmuth, James; Yeaman, Samuel
    The expansion of genomic technologies has uncovered profound insights into the physiology, etiology, demography, and treatment of disease in human and livestock populations alike. However, these advances have yet to be realized in wildlife due to the unique technical limitations inherent in these populations, including sample availability and quality. Concurrently, novel methods in genomics have been developed that are amenable for processing genetic samples obtained from wildlife. Specifically, target enrichment approaches have been developed that can amplify and genotype samples of low DNA mass, while genome imputation has been demonstrated as a viable approach for inferring missing genotype information at no incremental cost. Though these technologies may help bridge the gap between wildlife genetics and genomics, they have yet to be thoroughly validated in such populations. In this study, I tested a recently developed target enrichment approach, termed ‘Allegro Targeted Genotyping’ (ATG), as well as genome imputation in a population of free-living horses on Sable Island, Nova Scotia, Canada. For target enrichment, I evaluated the concordance between the output genotypes versus those obtained using standard genotyping approaches at the same set of genetic loci. I then determined the accuracy of genome imputation using existing genetic data from this population using different software as well as varying parameters including reference population size, initial genotype density and selection method for the initial genotypes. Genotypes from ATG were repeatable and concordant with standard genotyping panels, while imputation accuracy was generally high (>99%) and largely impacted by reference population size and initial density used for imputation. Both approaches proved successful and will help facilitate the study of population-wide genomics in Sable Island horses and may be generalizable to other wildlife study systems given further validation.
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    Genomic Signatures of Within-Generation Selection in Coho Salmon (Oncorhynchus kisutch) under Enriched Hatchery-Rearing Practices and in the Wild
    (2023-09-13) Bull, James Kenneth; Rogers, Sean Michael; Miller, Kristina; Munkittrick, Kelly Roland; Poissant, Jocelyn; Narum, Shawn
    Salmonids occupy central roles in the ecological and human communities in which they occur. As such, many salmonid populations are heavily managed for conservation and to support their harvest. This often involves hatcheries, which typically use captured mature adults to produce fertilized eggs which are reared to the smolt life-history stage, with resultant smolts released into the wild. Despite a history of over 150 years of hatchery use, fundamental questions remain about the ecological and evolutionary impacts of hatcheries on released fish and on the wild populations released fish interact with. Chief among these questions is the role and impact of selection in hatchery fish compared to wild fish and if domesticating processes are inevitable. In this thesis, I present a detailed investigation of the population genomics of an integrated hatchery-wild coho salmon (Oncorhynchus kisutch) population subjected to long-term experimental rearing under conventional hatchery environments, and under enriched hatchery environments designed to mimic aspects of the wild environment in efforts to mitigate potential effects of hatchery rearing. Specifically, I investigated (1) if spatial genetic structuring occurs among wild fish in this system, (2) if selection is detectable for survival-at-sea and for survival across the lifecycle within a single generation, and (3) if such selection depends on the rearing environment fish experience in the hatchery. I additionally reviewed what is known about gene expression under domestication in salmonids. I found no evidence for spatial genetic structuring among wild fish, indicating the typical strategy of restricted sampling of wild fish for inclusion in the hatchery broodstock should not drive differentiation between hatchery and wild fish. I also found evidence for within-generation selection for both survival-at-sea and survival across the lifecycle, and most importantly, that these signatures of selection differed between hatchery fish reared under different environments. Notably, signatures of selection for fish reared under enriched environments were not more similar to those observed in wild fish, compared to conventionally reared fish, indicating work remains in designing hatchery environments that mimic those aspects of the wild environment required to produce wild-like fish, and with implications for captive rearing programs more broadly.
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    Improved Resolution of Prevotella Species, Strains and Genes Reveals TheirDiversity and Virulence Potential in the Female Genital Tract
    (2021-01-29) Bagheri, Sahar; Sycuro, Laura K; Poissant, Jocelyn; Devinney, Rebekah; Lynch, Tarah; Geuking, Markus B
    Bacteria belonging to the genus Prevotella inhabit numerous human body sites, including the female genital tract. Although Prevotella species commonly, and often benignly colonize the vagina, their increased abundance is associated with the dysbiotic condition bacterial vaginosis (BV). Prevotella isolates are also routinely cultured from women experiencing upper genital tract infection and the genus has repeatedly been associated with preterm birth, but the ascending species and mechanisms involved are poorly understood. I developed a new bioinformatics tool that enabled me to ask, for the first time, whether genital Prevotella species encode the Type IX Secretion System, a feature that could contribute to their niche adaptation and virulence (Chapter II). The other objective of my thesis was to better define the phylogenetic breadth and genomic heterogeneity of Prevotella species that colonize the female genital tract. I sought to advance our understanding of how Prevotella impacts human pregnancy by: 1) Identifying the most prevalent and abundant Prevotella species in the lower vs. upper female genital tract; and 2) Performing the first comparative genomics study of the two most common vaginal Prevotella species, P. bivia and P. amnii, which have both been associated with preterm birth. I undertook these analyses using a multidisciplinary approach that included a systematic literature review (Chapter III), pangenome analysis (Chapter III), and a bioinformatics meta-analysis of 19 published microbiome datasets (Chapter IV). My research showed that genital Prevotella populations are much more diverse than previously appreciated, although relatively few genital Prevotella species were consistently detected in high abundance across cohorts. The correlated distribution of Prevotella species prevalence in the lower and upper genital tract suggests they may translocate via broadly conserved or passive mechanisms.The two most prevalent and closely related genital tract Prevotella species are genomically and functionally heterogeneous. Their distinct evolutionary history, driven by horizontal gene transfer and genome reduction, reflects both acquisition and loss of genes involved in evasion, adaptation, and niche partitioning. By expanding our understanding of genital Prevotella species diversity, and establishing parameters for their sensitive and specific detection, this work lays the foundation for future studies that will define the predictive and causal roles these enigmatic bacteria play in reproductive health.
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    Quantifying the impacts of inbreeding depression on adult reproductive success, survival, and foal birth in the feral horses (Equus ferus caballus) of Sable Island, Nova Scotia
    (2021-05-07) Jeong, Chanwoori; Poissant, Jocelyn; Musiani, Marco; Whiteside, Douglas
    Inbreeding, the mating between related individuals, often adversely affects individual fitness in a phenomenon known as inbreeding depression (ID). Small and genetically-isolated populations are especially vulnerable to ID, making understanding its causes and consequences important from a wildlife conservation perspective. Quantifying ID in wildlife is challenging, as there are difficulties with collecting long-term life history data needed to estimate fitness and high-quality genetic data needed to precisely estimate inbreeding, especially in free-living populations. In my thesis, I studied ID in the isolated feral horse population of Sable Island, Nova Scotia, by combining individual-based genomic, ecological and life history data from 239 individuals. Genomic data was generated using Single Nucleotide Polymorphism (SNP) arrays, and inbreeding levels were quantified through genomic estimators based on SNPs found in runs of homozygosity, FROH, correlation between uniting gametes, FUNI, and pairwise relatedness. I tested for presence of ID on sex-specific annual adult reproductive success and survival as well as foal births, and the influence of intrinsic and extrinsic variables in modulating ID using generalized linear mixed models and model averaging. Low overall levels of inbreeding was found in the population, and inbreeding was not a significant predictor of any of the fitness traits studied when considered on its own. However, results suggested that ID for female annual reproductive success, female annual survival, and male annual survival may be modulated by environmental conditions such as band size, location, and winter severity. The performance of the estimators FROH and FUNI were similar throughout my analyses. Using a standardized measure of ID, I also show that ID in Sable Island horses is relatively low in comparison to other wildlife populations. This research expands our knowledge of inbreeding depression in natural systems and provides Parks Canada with important information to assist with the management and conservation of Sable Island’s iconic population of feral horses.
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    Runs of homozygosity in Sable Island feral horses reveal the genomic consequences of inbreeding and divergence from domestic breeds
    (2022-07-12) Colpitts, Julie; McLoughlin, Philip D.; Poissant, Jocelyn
    Abstract Background Understanding inbreeding and its impact on fitness and evolutionary potential is fundamental to species conservation and agriculture. Long stretches of homozygous genotypes, known as runs of homozygosity (ROH), result from inbreeding and their number and length can provide useful population-level information on inbreeding characteristics and locations of signatures of selection. However, the utility of ROH for conservation is limited for natural populations where baseline data and genomic tools are lacking. Comparing ROH metrics in recently feral vs. domestic populations of well understood species like the horse could provide information on the genetic health of those populations and offer insight into how such metrics compare between managed and unmanaged populations. Here we characterized ROH, inbreeding coefficients, and ROH islands in a feral horse population from Sable Island, Canada, using ~41 000 SNPs and contrasted results with those from 33 domestic breeds to assess the impacts of isolation on ROH abundance, length, distribution, and ROH islands. Results ROH number, length, and ROH-based inbreeding coefficients (FROH) in Sable Island horses were generally greater than in domestic breeds. Short runs, which typically coalesce many generations prior, were more abundant than long runs in all populations, but run length distributions indicated more recent population bottlenecks in Sable Island horses. Nine ROH islands were detected in Sable Island horses, exhibiting very little overlap with those found in domestic breeds. Gene ontology (GO) enrichment analysis for Sable Island ROH islands revealed enrichment for genes associated with 3 clusters of biological pathways largely associated with metabolism and immune function. Conclusions This study indicates that Sable Island horses tend to be more inbred than their domestic counterparts and that most of this inbreeding is due to historical bottlenecks and founder effects rather than recent mating between close relatives. Unique ROH islands in the Sable Island population suggest adaptation to local selective pressures and/or strong genetic drift and highlight the value of this population as a reservoir of equine genetic variation. This research illustrates how ROH analyses can be applied to gain insights into the population history, genetic health, and divergence of wild or feral populations of conservation concern.
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    The ecology and fitness consequences of gut microbiome variation in Sable Island feral horses (Equus caballus)
    (2023-09-12) Stothart, Mason R.; Poissant, Jocelyn; Fox, Jeremy; McLoughlin, Philip Dunstan; Reimer De Bruyn, Raylene A; Wasmuth, James; Sycuro, Laura K; Archie, Elizabeth A
    Gut microbiomes are understood to be integral to the ecology and evolution of animal life, but until very recently, the scientific literature has lacked robust empirical characterization of the host genetic basis and fitness consequences of microbiome variation within wild animal populations. As a closed population of free-living but exhaustively surveyed fate-known individuals which are obligately reliant on their gut microbiomes, the feral horses of Sable Island (Nova Scotia) provide a tractable study system in which to study the ecology, host-to-host transmission, and fitness consequences of microbiome variation in the wild. In this thesis, I begin by characterizing the ecological determinants of the Sable Island horse hindgut microbiome (Chapter 2) and validate the use of shallow shotgun metagenomic sequencing methods for characterizing diverse microbial communities in the horse hindgut (Chapter 3). In applying a shallow shotgun metagenomic sequencing method to a dataset of 2394 fecal samples from 794 individuals spanning 7 years of collection, I find evidence that variation the gut microbiome is visible to host-level selection (Chapter 4). Further quantitative genetic analyses of these data reveal that microbiome features are weakly heritable on average (Chapter 5), suggesting a limited capacity for the microbiome to rapidly respond to selection; but animal model and eco-phylogenetic null model results independently provide evidence that the social dispersal of microbes between horses is an important determinant of microbiome structure. Furthermore, the microbiota which show the strongest evidence for social structuring are those which are most consequential for horse survival. These findings support hypotheses that non-genetic inheritance mechanisms (microbe dispersal) could critically underlie the ability for microbiomes to adaptively respond to selection on ecologically-relevant timescales. However, host inbreeding may constrain the capacity for microbiome variation to adaptively respond to host-level selection, since microbe responses to inbreeding were negatively associated with the estimated effects of those same microbiota on horse survival (Chapter 6). The proximate environmental and host genetic mechanisms underpinning microbiome variation, patterns of context-specific selection, and strain-level transmission remain to be characterized in detail. Nonetheless, this thesis contains tentative but important empirical milestones in describing the eco-evolutionary significance of host-associated microbiomes in the wild.