Galpern Lab @ Faculty of Environmental Design | University of Calgary

Software

We have developed and in most cases, published, several software packages to support our analyses in landscape connectivity and landscape genetics research. All of these use the statistical and scientific programming language R in one way or another.

 

 

MEMGENE

memgenefrag

Detect, visualize, and conduct inference on spatial genetic pattern with MEMGENE.

MEMGENE is a package for R that can detect relatively weak spatial genetic patterns using Moran’s Eigenvector Maps (MEM) to extract only the spatial component of genetic variation.  It has applications in landscape genetics where the movement and dispersal of organisms are studied using neutral genetic variation.

It is available on CRAN, and has been published with tutorials and extensive supplementary material in Methods in Ecology and Evolution.

The analytical aspects of MEMGENE were developed in collaboration with Pedro Peres-Neto (UQAM).

 

 

ALLELEMATCH

ALLELEMATCH is a package for  R that identifies unique genotypes and is particularly helpful for non-invasive sampling applications (e.g. where fecal or hair material is collected).  ALLELEMATCH is available on CRAN and is published in Molecular Ecology Resources and has been applied for a range of applications including to support genetic capture-mark-recapture, to identified plant clones and to match tadpole samples to adult frogs.

How many animals are there? Use ALLELEMATCH to identify unique genotypes when there are multiple samples from the same individual, and genotyping error or missing data can make things difficult

 

GRAINSCAPE

Build landscape networks, find shortest paths, summarize properties of these networks, and visualize the result with GRAINSCAPE.

GRAINSCAPE is also an R package for developing grains of connectivity and minimum planar graphs of landscape connectivity. A detailed tutorial is available here.  GRAINSCAPE is hosted at the secondary R repository, R-forge and thanks to Andrew Fall is distributed with his binary, SELES. Instructions to download, install, as well as manuals and tutorials are available here.

Although it has not itself been published in a journal, it is used in three papers (Galpern et al., 2012, Molecular Ecology; Galpern & Manseau, 2013, Landscape Ecology; Galpern & Manseau, 2013, Ecography).

 

 

POPSCAPE

popscapeAtWork

Simulate the effect of landscape on movement, dispersal and gene flow with POPSCAPE.

POPSCAPE is a landscape genetic simulation engine written partly in R and partly in the agent-based modelling framework NetLogo.  It enables the programming of agents (representing individuals and their genes) and allows them to move and mate anywhere within a pre-defined world.

A resistance surface, describing the hypothesized influence on gene flow by landscape features can be included.  Demographic and vagility parameters can also be manipulated.  It is used and presented in an appendix of the MEMGENE paper in Methods in Ecology and Evolution.  If you would like to use this code, please get in touch.

 

 

 

MICROSATSERVER

MicroSatServer is a database web application that with collaborators Micheline Manseau (Parks Canada & University of Manitoba) and Paul Wilson (Trent University), we use to manage and coordinate genetic data for almost 10 000 caribou fecal pellet samples. The link contains a PDF summarizing its features. If you are interested in developing your own version of MicroSatServer, please contact me, and I will share source code!

Noteworthy

JUL 17/07 University of Calgary is using our bumble bee and climate change work as part of a national advertising campaign. See this poster snapped as we sped by on Calgary Transit. Our part of the campaign can be found here

JUN 13/17: Summer is here, and we have started sampling in canola fields and in ditches in the Calgary area, near Duchess, and near Claresholm, Alberta. Big thanks to our grower-cooperators who allow us into their fields to sample insects and measure yield. And also to Canola Council of Canada, Ducks Unlimited Canada, Alberta Biodiversity Monitoring Institute and Alberta Conservation Association whose ongoing support has enabled us to expand this prairie cropland ecosystem services and conservation program.

JUN 8/17: We have been in the news. Here our beneficial insect project coordinator Jess Vickruck and Canola Council agronomist Gregory Sekulic talk to Grainews about our collaborative prairie research project. University of Calgary also reported recently on our bee work, here.
APR 1/17: Our field program is building. We have FOUR paid positions this summer for our various Prairie beneficial insect projects. Please contact Jess Vickruck if you are interested in applying. [Thank you for your interest. All positions are now filled. Closed.]

APR 5/16: We have THREE paid positions for field/lab assistants on our pollinator landscape ecology projects. See here for more information. Apply soon. [Thanks to those who applied. Now closed.]

DEC 14/15: It's always Bombus rufocinctus! We are looking for undergraduate volunteers starting in the new year to help us identify bumble bees from this summer's field collection. 1picrufo The infamous and abundant rufocinctus is anything but red-belted as the latin scholars among you have already suggested. Rather, it is a brilliant mimic with thirteen different colour pattern morphs that make our game of identifying prairie bumble bees especially fun. Fortunately we have a secret up our sleeve. Come join the rufocinctus gang and find out how to tell a real rufo (err--we think). Thanks to artist and bee ecologist Riley Waytes for our mascot.

OCT 26/15: University of Calgary tweets about our bumble bee climate change study as one of five "research advances that could change our world." There's always hope!

SEP 15/15: Very pleased to be advertising for a University of Calgary Eyes High Postdoctoral Scholar in pollinator informatics--or is that bee-o-informatics? See the job posting here.

JULY 16/15: We're quite excited about our team's new bumble bee climate change study just out in Science (Kerr, Pindar, Galpern, et al., 2015). The findings were covered by over 400 media outlets around the world (here's a list), with stories appearing in print, on the web, on the radio, in streaming video, on several Canadian TV networks, and in a few languages.

JULY 10/15: Here's University of Calgary's coverage of the main findings of our new bumble bee climate change study in Science.

MAY 1/15: We are advertising for several graduate positions in pollinator conservation and in landscape modelling (for caribou). Please read the ads here. Applications accepted immediately until filled. Start dates as early as Fall 2015 are possible.

APR 14/15 We are advertising for TWO summer field assistants to help with our landscape-scale pollinator field experiment. Please email Paul Galpern to inquire. UPDATE: These positions have now been filled.

APR 14/15 We are advertising for a summer research assistant to take a lead role in our walkshed project. Please see the job ad here. UPDATE: This position has now been filled.

FEB 1/15: We are gearing up for our summer pollinator field experiment in the Calgary area where we will look at how landscape context has influenced insect pollinators. We are also looking for volunteers to help us collect samples from insect traps.

DEC 1/14 We're looking for graduate students. Get in touch if you have any overlapping interests!

AUG 16/14: MEMGENE, new software for detecting, visualizing and conducting inference on spatial genetic data is now published in Methods in Ecology and Evolution. The package is available on CRAN. Helpful for landscape genetics!