Applied Filters
- Ecology and Evolution
- Genetics and GenomicsRemove filter
- FACETSRemove filter
Publication Date
Author
- Burles, Douglas W2
- Davy, Christina M2
- Dogantzis, Kathleen2
- Donaldson, Michael E2
- Jung, Thomas S2
- Kim, Jin-Hong2
- Kyle, Christopher J2
- Lausen, Cori L2
- McAlpine, Donald F2
- McBurney, Scott2
- Miller, Kristina M2
- Mitchell, Greniqueca2
- Mordecai, Gideon2
- Park, Allysia2
- Patterson, Brent R2
- Redquest, Bridget2
- Rico, Yessica2
- Ritchie, Kyle2
- Rutledge, Linda Y2
- Schulze, Angela2
- Tabata, Amy2
- Vanderwolf, Karen J2
- Willis, Craig K R2
- Wilson, Paul J2
- Addison, Jason A1
Access Type
1 - 11of11
Save this search
Please login to be able to save your searches and receive alerts for new content matching your search criteria.
Filters
You do not have any saved searches
- OPEN ACCESSWe report the development of an improved method for the extraction and amplification of leaf miner DNA recovered from empty mines. Our method is simple, easy to use, and foregoes the time-consuming task of scraping out mines required by previous methods. We collected leaves with 1- and 2-day-old vacated mines, cut out and then ground the mined portions, and amplified the mtDNA COI barcode sequence using universal insect primers. We obtained high-quality sequences for 31% of our empty mines: 20% yielded sequences associated with a leaf miner species; and an additional 11% yielded sequences associated with whiteflies, mites, or fungi. Our improved method will facilitate ecological studies determining herbivore community dynamics and agricultural studies for pest monitoring and identification.
- OPEN ACCESSThe need to better understand how plasticity and evolution affect organismal responses to environmental variability is paramount in the face of global climate change. The potential for using RNA sequencing (RNA-seq) to study complex responses by non-model organisms to the environment is evident in a rapidly growing body of literature. This is particularly true of fishes for which research has been motivated by their ecological importance, socioeconomic value, and increased use as model species for medical and genetic research. Here, we review studies that have used RNA-seq to study transcriptomic responses to continuous abiotic variables to which fishes have likely evolved a response and that are predicted to be affected by climate change (e.g., salinity, temperature, dissolved oxygen concentration, and pH). Field and laboratory experiments demonstrate the potential for individuals to respond plastically to short- and long-term environmental stress and reveal molecular mechanisms underlying developmental and transgenerational plasticity, as well as adaptation to different environmental regimes. We discuss experimental, analytical, and conceptual issues that have arisen from this work and suggest avenues for future study.
- OPEN ACCESS
- Christina M. Davy,
- Michael E. Donaldson,
- Yessica Rico,
- Cori L. Lausen,
- Kathleen Dogantzis,
- Kyle Ritchie,
- Craig K.R. Willis,
- Douglas W. Burles,
- Thomas S. Jung,
- Scott McBurney,
- Allysia Park,
- Donald F. McAlpine,
- Karen J. Vanderwolf, and
- Christopher J. Kyle
The fungus that causes bat white-nose syndrome (WNS) recently leaped from eastern North America to the Pacific Coast. The pathogen’s spread is associated with the genetic population structure of a host (Myotis lucifugus). To understand the fine-scale neutral and immunogenetic variation among northern populations of M. lucifugus, we sampled 1142 individuals across the species’ northern range. We used genotypes at 11 microsatellite loci to reveal the genetic structure of, and directional gene flow among, populations to predict the likely future spread of the pathogen in the northwest and to estimate effective population size (Ne). We also pyrosequenced the DRB1-like exon 2 of the class II major histocompatibility complex (MHC) in 160 individuals to explore immunogenetic selection by WNS. We identified three major neutral genetic clusters: Eastern, Montane Cordillera (and adjacent sampling areas), and Haida Gwaii, with admixture at intermediate areas and significant substructure west of the prairies. Estimates of Ne were unexpectedly low (289–16 000). Haida Gwaii may provide temporary refuge from WNS, but the western mountain ranges are not barriers to its dispersal in M. lucifugus and are unlikely to slow its spread. Our major histocompatibility complex (MHC) data suggest potential selection by WNS on the MHC, but gene duplication limited the immunogenetic analyses. - OPEN ACCESSDistinguishing between intra- and inter-specific variation in genetic studies is critical to understanding evolution because the mechanisms driving change among populations are expected to be different than those that shape reproductive isolation among lineages. Genetic studies of north Atlantic green sea urchins Strongylocentrotus droebachiensis (Müller, 1776) have detected significant population substructure and asymmetric gene flow from Europe to Atlantic Canada and interspecific hybridization between S. droebachiensis and Strongylocentrotus pallidus (Sars, 1871). However, combined with patterns of divergence at mtDNA sequences, morphological divergence at gamete traits suggests that the European and North American lineages of S. droebachiensis may be cryptic species. Here, we use a combination of cytochrome c oxidase subunit I (COI) sequences and single nucleotide polymorphisms (SNPs) to test for cryptic species within Strongylocentrotus sea urchins and hybrids between S. droebachiensis and S. pallidus populations. We detect striking patterns of habitat and reproductive isolation between two S. droebachiensis lineages, with offshore deep-water collections consisting of S. pallidus in addition to a cryptic lineage sharing genetic similarity with previously published sequences from eastern Atlantic S. droebachiensis. We detected only limited hybridization among all three lineages of sea urchins, suggesting that shared genetic differences previously reported may be a result of historical introgression or incomplete lineage sorting.
- OPEN ACCESS
- OPEN ACCESSThe salmon louse Lepeophtheirus salmonis (Krøyer 1837) displays numerous sexually dimorphic characteristics. Insights into their underlying molecular components have only recently been explored, which serve to better understand both the basic biology of the louse, associated impacts on drug sensitivity, and evolution of resistance. Expression of 16 L. salmonis genes putatively involved in sexual dimorphism and reproduction were used to determine differences between sexes and better understand responses to mating using RT-qPCR of pre-adult and adult lice. Analysis of these genes revealed the dynamic nature of sex-biased expression across stages. However, female reception of a spermatophore did not appear to impact the expression of these particular genes. Furthermore six of these transcripts and 84 others identified previously in a large-scale louse transcriptomics experiment were used to estimate differences in evolutionary rates and codon-usage bias of sex-related genes using phylogenetic analysis by maximum likelihood (PAML) and codonW. Results suggest male-biased genes are evolving at significantly greater rates than female-biased and unbiased genes as evidenced by higher rates of non-synonymous substitutions and lower codon-usage bias in these genes. These analyses expand our understanding of interactions of sex-biased expression across the pre-adult and adult life stages and provide foundations for better understanding evolutionary differences in sex-biased genes of L. salmonis.
- OPEN ACCESS
- Amy K. Teffer,
- Jonathan Carr,
- Amy Tabata,
- Angela Schulze,
- Ian Bradbury,
- Denise Deschamps,
- Carole-Anne Gillis,
- Eric B. Brunsdon,
- Gideon Mordecai, and
- Kristina M. Miller
Infectious agents are key components of animal ecology and drivers of host population dynamics. Knowledge of their diversity and transmission in the wild is necessary for the management and conservation of host species like Atlantic salmon (Salmo salar). Although pathogen exchange can occur throughout the salmon life cycle, evidence is lacking to support transmission during population mixing at sea or between farmed and wild salmon due to aquaculture exposure. We tested these hypotheses using a molecular approach that identified infectious agents and transmission potential among sub-adult Atlantic salmon at marine feeding areas and adults in three eastern Canadian rivers with varying aquaculture influence. We used high-throughput qPCR to quantify infection profiles and next generation sequencing to measure genomic variation among viral isolates. We identified 14 agents, including five not yet described as occurring in Eastern Canada. Phylogenetic analysis of piscine orthoreovirus showed homology between isolates from European and North American origin fish at sea, supporting the hypothesis of intercontinental transmission. We found no evidence to support aquaculture influence on wild adult infections, which varied relative to environmental conditions, life stage, and host origin. Our findings identify research opportunities regarding pathogen transmission and biological significance for wild Atlantic salmon populations. - OPEN ACCESS
- Christoph M. Deeg,
- Albina N. Kanzeparova,
- Alexei A. Somov,
- Svetlana Esenkulova,
- Emiliano Di Cicco,
- Karia H. Kaukinen,
- Amy Tabata,
- Tobi J. Ming,
- Shaorong Li,
- Gideon Mordecai,
- Angela Schulze, and
- Kristina M. Miller
Salmon are keystone species across the North Pacific, supporting ecosystems, commercial opportunities, and cultural identity. Nevertheless, many wild salmon stocks have experienced significant declines. Salmon restoration efforts focus on fresh and coastal waters, but little is known about the open ocean environment. Here we use high throughput RT-qPCR tools to provide the first report on the health, condition, and infection profile of coho, chum, pink, and sockeye salmon in the Gulf of Alaska during the 2019 winter. We found lower infectious agent number, diversity, and burden compared with coastal British Columbia in all species except coho, which exhibited elevated stock-specific infection profiles. We identified Loma sp. and Ichthyophonus hoferi as key pathogens, suggesting transmission in the open ocean. Reduced prey availability, potentially linked to change in ocean conditions due to an El Niño event, correlated with energetic deficits and immunosuppression in salmon. Immunosuppressed individuals showed higher relative infection burden and higher prevalence of opportunistic pathogens. We highlight the cumulative effects of infection and environmental stressors on overwintering salmon, establishing a baseline to document the impacts of a changing ocean on salmon. - OPEN ACCESS
- Greniqueca Mitchell,
- Paul J. Wilson,
- Micheline Manseau,
- Bridget Redquest,
- Brent R. Patterson, and
- Linda Y. Rutledge
Woodland caribou (Rangifer tarandus caribou) are threatened in Canada because of the drastic decline in population size caused primarily by human-induced landscape changes that decrease habitat and increase predation risk. Conservation efforts have largely focused on reducing predators and protecting critical habitat, whereas research on dietary niches and the role of potential food constraints in lichen-poor environments is limited. To improve our understanding of dietary niche variability, we used a next-generation sequencing approach with metabarcoding of DNA extracted from faecal pellets of woodland caribou located on Lake Superior in lichen-rich (mainland) and lichen-poor (island) environments. Amplicon sequencing of fungal ITS2 region revealed lichen-associated fungi as predominant in samples from both populations, but amplification at the chloroplast trnL region, which was only successful on island samples, revealed primary consumption of yew (Taxus spp.) based on relative read abundance (83.68%) with dogwood (Cornus spp.; 9.67%) and maple (Acer spp.; 4.10%) also prevalent. These results suggest that conservation efforts for caribou need to consider the availability of food resources beyond lichen to ensure successful outcomes. More broadly, we provide a reliable methodology for assessing ungulate diet from archived faecal pellets that could reveal important dietary shifts over time in response to climate change. - OPEN ACCESSThe lake whitefish (Coregonus clupeaformis) is a commercially valuable freshwater species with a broad distribution in North America. Some phylogeographic work has been done on this species, but little is known about genetic population subdivision among populations of the widely dispersed Mississippian lineage. We used 3,173 single nucleotide polymorphisms in 508 lake whitefish from 22 different lakes to examine population structure across central Canada and the United States. Bayesian clustering, ordination, and fixation indices identified population subdivision that largely reflected geographic distance and hydrological connectivity, with greater differentiation between lakes that are farther apart. Population subdivision was hierarchical, with greater differentiation between Canadian provinces and less differentiation based on river basins within provincial boundaries. Interestingly, isolation by distance alone was not sufficient to account for all of the observed genetic differentiation among populations. We conclude that important components of lake whitefish genetic diversity are present at different spatial scales, and that populations within the Mississippian lineage have differentiated widely across their range.
- OPEN ACCESS