Prospective Students

Contact Info
Dr. Stephen C. Lougheed
Department of Biology
Queen's University
Kingston, Ontario
Canada K7L3N6
Telephone: 613-533-6128
FAX: 613-533-6617
email: steve.lougheed@queensu.ca

| Postdoctoral | Graduate | Undergraduate |

POSTDOCTORAL

Gjoa_Haven_November

Gjoa Haven in November. Photo Peter de Groot.

Postdoctoral position fisheries genomics.
We seek a motivated individual to manage a large-scale fisheries genomics project (http://arcticfishery.ca/). The incumbent will coordinate sampling and sequencing of several thousand arctic char, arctic cod, and northern shrimp for the purpose of defining and understanding stock populations and dynamics. He/she will work with the PIs to establish analysis pipelines and support several graduate students who will further use these data for their own specific project goals. Prior project management and next-gen sequencing data analysis experience are key. The candidate will be part of a team of researchers seeking to contribute to a community- and science-based Nunavut sustainable fisheries. Biology, Queen’s University is dynamic and collaborative department with 36 tenured or tenure-track faculty, well-equipped molecular and microscopy facilities, multiple well-attended seminar series, and one of the best field stations in Canada (http://biology.queensu.ca/). Queen’s University is located in the centre of the small, historic city of Kingston, Ontario, on the northern shores of Lake Ontario.

Education requirements:
• PhD in computational biology/bioinformatics OR statistics/computer science/math/engineering background with a firm grasp of genomics and genetics

Required background/experience:
• published Next-Gen sequencing data analysis: familiarity with public alignment pipelines, SNV calling algorithms, common NGS manipulation tools and standardized NGS data formats (e.g. SAM/BAM, VCF) and genome assembly (e.g. ALLPATHS, SOAPdenovo)
• competent programmer fluent in Unix/Linux, Perl or Python, and R or Matlab
• computer cluster operation (e.g. PBS, LSF, Torque)
• experience managing large datasets (Tbs)
• managing personnel in the lab and mentoring students
• strong interpersonal and communication skills
• excellent oral and written English communication skills
• outstanding academic and professional track record, including presentations at international conferences and experience producing high quality published research

Additional desirable experience:
• ddRAD-Seq
• evolutionary ecology

Salary:
$65,000 CDN plus benefits

Duration:
2 years

Application:
Interested applicants should contact Stephen Lougheed (steve.lougheed@queensu.ca) directly. Please include 1) your CV that highlights the relevant skills, 2) a one-paragraph summary of your career goals and why you’d like to lead this effort, 3) names of three references and their contact information. Open until a suitable candidate is found.  Preferred start: January or February 2016.

 

GRADUATE

PhD positions in fisheries genomics & conservation.

A previous mode of transport. Photo by Peter de Groot.

A previous mode of transport. Photo by Peter de Groot.

We seek to fill three Ph.D. positions that each focus on the genomics of three arctic species – Arctic char, Arctic cod, and Northern shrimp – from the Lower Northwest Passage in the Canadian Arctic. Each student will assemble and analyze a dataset of genomic markers from wild caught individuals and deploy a range of statistical and spatial approaches to help define independent stocks, and explore population connectivity and past demographic history. There will be lots of scope for innovative approaches to data analyses, spanning seascape genetics through simulation modelling. The results from these analyses colelctively will be used to help understand the potential consequences of a dramatically changing Canadian Arctic on marine biodiversity and inform future fisheries management and conservation. Candidates will be part of a well-funded team of researchers seeking to contribute to a community- and science-based Nunavut sustainable fisheries. The Department of Biology at Queen’s University (http://biology.queensu.ca/) is dynamic and collaborative department with 36 tenured or tenure-track faculty, well-equipped molecular and microscopy facilities, multiple well-attended seminar series, and one of the best field stations in Canada (http://www.queensu.ca/qubs/). Queen’s University is located in the centre of the small, historic city of Kingston, Ontario, on the northern shore of Lake Ontario.

Education requirements:
• M.Sc. in biology or related discipline preferable with knowledge of genetics, genomics, and/or bioinformatics OR B.Sc. with first class standing with similar background.

Skills & experience:
• strong interpersonal and communication skills
• excellent oral and written English communication skills
• strong academic track record
• familiarity with theory and applications in evolutionary and population genetics/genomics
• familiarity with statistics and data analysis

Additional desirable experience:
• some experience with ddRAD-Seq or Genotyping-by-Sequencing data
• familiarity with GIS analytical tools
• experience with some Next Gen Sequencing data

Note that we will provide training in all of these.

Duration:
Stipend and research support for 4 years with opportunities to develop teaching and mentorship skills.

Application:
Interested applicants should contact Stephen Lougheed (steve.lougheed@queensu.ca) directly. Please include 1) your CV that highlights the relevant skills, 2) a one-paragraph summary of your career goals and why you would like to undertake a PhD at Queen’s, 3) names of three references and their contact information. Start dates: January through September 2016.

 

UNDERGRADUATE

Prospective Undergraduate Thesis Students

We will host 1 or 2 undergraduate thesis students in our lab in the 2016-17 school year. We have a large lab with a variety of on-going projects spanning speciation to conservation genomics. Below we list three possible areas of research any of which would provide rich experience for an undergraduate thesis.

1. Fish genomics

Char from springtime nets. Photo by Peter de Groot.

Char from springtime nets. Photo by Peter de Groot.

Central to such ecologically-sound and sustainable fishing practices, is an understanding of the stock populations and their genetic and adaptive differences. Failure to manage fisheries on good science can have catastrophic consequences most obviously evidenced in recent years by the collapse of the east coast Atlantic cod fisheries. Dr. Lougheed and colleagues were recently awarded funding from Genome Canada to use leading-edge genomics and bioinformatics to define fish stocks (http://arcticfishery.ca/). We will map and interpret the genomic diversity of wild Lower Northwest Passage populations of Arctic char, Arctic cod, and a shrimp species, taxa that have the most promise for a managed fishery. The goal is to sequence the genomes of focal species and to develop species-specific single nucleotide polymorphism (SNPs) using next generation sequencing methods, work that will be undertaken by graduate students, a postdoctoral fellow, and an undergraduate summer student. These genomic data will be integrated with traditional ecological knowledge (TEK) to develop a sustainable management of these emerging fisheries, facilitating the development of commercial opportunities, increasing employment, providing a healthy food source and food security, and contributing to increased prosperity and well-being for the people of Nunavut. This project would focus on quantifying patterns of differentiation among different sampled char populations and interpreting their recent evolutionary and population dynamics.

2. Frog speciation

Wood frog. Photo by S.C. Lougheed.

Wood frog. Photo by S.C. Lougheed.

One of the most enduring goals in evolutionary biology is to understand how new species arise. The traditional view, popularized by 20th Century evolutionary biologist Ernst Mayr, emphasized a geographic view of speciation where most new species arise or at least begin through physical and thus genetic isolation of ancestral populations. Recent theoretical and empirical work has moved away from these geography-based views of speciation to ones that emphasize mechanism (e.g. selection driving ecological divergence) producing important insights into how new species arise. However, our own research over the last 5 years highlights the pervasiveness of both geographic isolation and subsequent secondary contact in the histories of most vertebrate species, mirroring comprehensive reviews of the phylogeographic literature. Our NSERC-funded research focuses on a single temperate North American frog, the spring peeper (Pseudacris crucifer). Our published work suggests that the spring peeper has a dynamic evolutionary history with 6 well-supported evolutionary lineages that originated in distinct, isolated refugia between 11 and 3 million years before present. Different lineage pairs with disparate times of divergence have come into secondary contact in different parts of the species’ range, presumably within the last 10-15,000 years. We are tackling a series of questions one of which might help frame a 537 project: (i) What is the relation of divergence times between evolutionary lineages and patterns of reproductive isolation, the hallmark of biological species? (ii) What do genomic data say about the patterns of gene flow among lineages over the entire history of this species? (iii) Does secondary contact enhance reproductive barriers of closely-related lineages, either to diminish acoustic interference of male advertisement calls used by females in mate selection, or to prevent maladaptive hybridization? (iv) How might marked differences in the acoustic environment or seasonality shape the outcomes of secondary contact between diverging lineages? (v) What are the various fitness costs of hybridization between lineages?

3. Reptile landscape genetics

Chris, Amanda and Jeff with foxsnakes. Photo by S.C. Lougheed.

Chris, Amanda and Jeff with foxsnakes. Photo by S.C. Lougheed.

Landscape genetics and increasingly genomics have proved indispensible in augmenting our understanding of how physical and biotic environmental features modulate dispersal, gene flow, and local adaptation. We have embraced these approaches combining molecular surveys, GIS and spatially-explicit simulations, and detailed radiotelemetry and demographic studies. Our Ontario work focuses on reptiles of conservation concern, evaluating the impact of habitat fragmentation on population connectivity and persistence. This work collectively shows far greater genetic subdivision within the distributions of focal Canadian species than would be predicted based on apparent distribution, and implies that habitat loss and degradation threaten their persistence over much if their respective ranges. We have assembled samples from a range of species-at-risk snakes from across Ontario but focused on southwestern Ontario and the eastern shores of Georgian Bay, and are working to quantify patterns of diversity and genetic differentiation as they relate to past and present landscape usage and fragmentation. The ultimate goal is to both understand how human-induced changes to habitat have impacted the probability of species persistence and how we might mitigate these impacts.

4. Grassland bird habitat modeling

Loggerhead shrike. Photo by Larry Kirtley.

Loggerhead shrike. Photo by Larry Kirtley.

Habitat loss and degradation are two of the most significant and widespread factors contributing to species declines and extinction. In North America, native prairie and grassland habitats have suffered some of the greatest losses – less than 1% of tallgrass prairie remains, and mixed-grass and short-grass prairie have been reduced to 20-30% of their former extent. Fifty-seven percent of North American grassland bird species are undergoing significant, long-term population declines. Thus far, conservation efforts have focused primarily on breeding habitat, but they have not been able to reverse population declines. The role of threats faced during the wintering season is believed to be important, but it has received relatively little attention. Our lab has been working to quantify migratory connectivity and develop a full annual life cycle model for the Loggerhead Shrike, a species associated with grassland habitat, has experienced the 6th most drastic population decline of any landbird species over the life of the Breeding Bird Survey. We have amassed wintering season territory locational data for more than 900 shrikes. Each bird has been distinguished as migrant or resident using stable isotopes and genetic data. This massive data set will be used to develop a spatially explicit model of winter habitat use for Loggerhead Shrike. The ultimate goal is to help the North American Loggerhead Shrike Working Group develop standardized methodology that can be applied across the species range and used as the basis of further study of winter season demographics and limiting factors.