113 Works

Supplemental material for: The dynamics of bird diversity in the new world

Antonin Machac
Three prominent explanations have been proposed to explain the dramatic differences in species richness across regions and elevations, (1) time for speciation, (2) diversification rates, and (3) ecological limits. But the relative importance of these explanations and, especially, their interplay and possible synthesis remain largely elusive. Integrating diversification analyses, null models, and GIS, I study avian richness across regions and elevations of the New World. My results reveal that even though the three explanations are...


Kyle Larson
Simple R scripts for plotting and processing trend an plunge data with an emphasis on quartz c-axes. Enables the generation of scatter plots, contour plots, determination of fabric opening angles and fabric strength parameters.

Disconnects between ecological theory and data in phenological mismatch research

Heather Kharouba & Elizabeth Wolkovich
Climate change may lead to phenological mismatches, where the timing of critical events between interacting species becomes de-synchronized, with potential negative consequences. Evidence documenting negative impacts on fitness is mixed. The Cushing match-mismatch hypothesis, the most common hypothesis underlying these studies, offers testable assumptions and predictions to determine consequences of phenological mismatch when combined with a pre-climate change baseline. Here, we highlight how improved approaches could rapidly advance mechanistic understanding. We find that currently no...

Summer workshop 1: Reproducible research through Open Science

Jason Pither, Mathew Vis-Dunbar, Sarah Amundrud, Bruno Carturan, Mauro Sugawara & Samantha Straus
This hosts materials associated with an online webinar introducing the core concepts of Open Science and Reproducibility, and providing an introduction to the OSF online collaboration platform

TASA Cheque Day Study

Lindsey Richardson
Randomized field experiment testing whether varying the timing and frequency of income assistance payments could reduce payment coincident increases in drug use and drug-related harm

Data from: Life history variation in an invasive plant is associated with climate and recent colonization of a specialist herbivore

Jennifer L. Williams & Sophie S. Duncan
Premise: Spatial variation in selective pressures can lead to intraspecific variation in life history, favoring some life histories and constraining others depending on the vulnerability of life stages. We examined how spatial variation in herbivory and climate influences flowering size and the occurrence of semelparity (reproducing once) versus iteroparity (reproducing multiple times) in the introduced range of an invasive plant, houndstongue (Cynoglossum officinale). Houndstongue is a short-lived semelparous perennial in its native range. In its...

Investigating morphological complexes using informational dissonance and bayes factors: A case study in corbiculate bees

Diego Porto, Eduardo Almeida & Matthew Pennell
It is widely recognized that different regions of a genome often have different evolutionary histories and that ignoring this variation when estimating phylogenies can be misleading. However, the extent to which this is also true for morphological data is still largely unknown. Discordance among morphological traits might plausibly arise due to either variable convergent selection pressures or else phenomena such as hemiplasy. Here we investigate patterns of discordance among 282 morphological characters, which we scored...

The genome of Draba nivalis shows signatures of adaptation to the extreme environmental stresses of the Arctic

Michael Nowak, Siri Birkeland, Terezie Mandáková, Rimjhim Roy Choudhury, Xinyi Guo, Lovisa Gustafsson, Abel Gizaw, Audun Schrøder-Nielsen, Marco Fracassetti, Anne Brysting, Loren Rieseberg, Tanja Slotte, Christian Parisod, Martin Lysak & Christian Brochmann
The Arctic is one of the most extreme terrestrial environments on the planet. Here we present the first complete genome assembly of a plant adapted to the high Arctic, Draba nivalis (Brassicaceae), an attractive model species for studying plant adaptation to the stresses imposed by this harsh environment. We used an iterative scaffolding strategy with data from short-reads, single-molecule long reads, proximity ligation data, and a genetic map to produce a 302 Mb assembly that...

A study of tactical and sexual dimorphism in cognition with insights for sexual conflict

Hannah Griebling, Oscar Rios-Cardenas, Jessica Abbott & Molly Morris
The sexes may have different optima in cognitive traits due to differences in life history strategies and the expense of investing in metabolically costly brain tissue. However, given genetic correlations, each sex could be constrained from reaching its cognitive optimum due to intralocus sexual conflict. We compared learning performance of two male alternative reproductive tactics and females from known genotypes (both sire and dam) in the livebearing fish Xiphophorus multilineatus. We predicted that females’ learning...

Session 4 Re-Introduction to the Data Life Cycle

Mathew Vis-Dunbar, Nick Rochlin, Marjorie Mitchell, Allan Cho, Doug Brigham, Susan Paterson, Susan Atkey, Mayu Ishida, Sheryl Adam, Sarah Parker, Elizabeth Kinney, George Parker, Megan Meredith-Lobay, Jiarui Li & Eugene Barsky


Kyle Larson
Scripts for plotting geochronological and petrochronological data in R

Long-term logging residue loadings affect tree growth but not soil nutrients in lodgepole pine forests

Jianping Wu, Xiaohua Wei, Michaela Waterhouse & Guang Qi
Both above- and below-ground characteristics are affected by logging residue loadings. Long-term monitoring of tree growth and soil nutrients was conducted. We found that tree growth but not soil nutrients were affected. There were dynamic relationships between tree growth and logging residue loadings.

Data from: Genotyping-in-Thousands by sequencing reveals marked population structure in Western Rattlesnakes to inform conservation status

Danielle Schmidt, Purnima Govindarajulu, Karl Larsen & Michael Russello
Delineation of units below the species level is critical for prioritizing conservation actions for species at-risk. Genetic studies play an important role in characterizing patterns of population connectivity and diversity to inform the designation of conservation units, especially for populations that are geographically isolated. The northernmost range margin of Western Rattlesnakes (Crotalus oreganus) occurs in British Columbia, Canada, where it is federally classified as threatened and restricted to five geographic regions. In these areas, Western...

EPIC-SCI Trial Protocol: Supplements

Femke Hoekstra, Joan Úbeda-Colomer, Miranda Dinwoodie, Gabriel Dix, Emily Giroux, Sarah Lawrason, Kendra Todd, Jan van der Scheer, Kathleen Ginis, Bobo Tong & Kenedy Olsen
Supplementary files related to EPIC-SCI protocol paper.

Data and Scripts for: Potential for long-distance dispersal of freshwater diatoms adhering to waterfowl plumage

Jason Pither & Faye Manning
This public repository hosts the data and scripts associated with the article "Potential for long-distance dispersal of freshwater diatoms adhering to waterfowl plumage"

Combining agent-based, trait-based and demographic approaches to model coral community dynamics - Data and scripts

Bruno Carturan, Jason Pither & Lael Parrott
We provide here all the information, datasets and R and Repast scripts related to the manuscript and appendices.

Validation HAIS-Q Spanish

J. Delgado-Ron

Changes in soil fungal communities following anthropogenic disturbance are linked to decreased lodgepole pine seedling performance

Jackson Beck, Jon Cale, Jean Rodriguez-Ramos, Sanat Kanekar, Justine Karst, James Cahill, Suzanne Simard & Nadir Erbilgin
Summary 1. Disturbances are frequent events across the Canadian boreal forest and can affect both below and above ground ecosystem processes. How disturbances change belowground soil fungal communities and in-turn affect pine establishment and performance is poorly understood. Such understanding has become increasingly important in-light-of observed changes in disturbance regimes in recent years due to climate change. 2. We used a greenhouse experiment to determine how soil inoculum collected from lodgepole pine stands undisturbed (control)...

Phylogenetic analysis of the distribution of deadly amatoxins among the little brown mushrooms of the genus Galerina

Mary Berbee, Brandon Landry, Jeannette Whitton, Anna Bazzicalupo & Oldriska Ceska
Some but not all of the species of 'little brown mushrooms' in the genus Galerina contain deadly amatoxins at concentrations equaling those in the death cap, Amanita phalloides. However, Galerina's ~300 species are notoriously difficult to identify by morphology and the identity of toxin-containing specimens has not been verified with DNA barcode sequencing. This left open the question of which Galerina species contain toxins and which do not. We selected specimens for toxin analysis using...

Data for: Coevolution fails to maintain genetic variation in a host-parasite model with constant finite population size

Ailene MacPherson, Matthew Keeling & Sarah Otto
Coevolutionary negative frequency-dependent selection has been hypothesized to maintain genetic variation in host and parasites. Despite the extensive literature pertaining to host-parasite coevolution, the dynamics of genetic variation has not been examined in a matching-alleles model (MAM) with a finite population size relative to the expectation under neutral genetic drift alone. The dynamics of the MA coevolution in an infinite population, in fact, suggests that genetic variation in these coevolving populations behaves neutrally. By comparing...

Data from: Beyond a single patch: local and regional processes explain diversity patterns in a seagrass epifaunal metacommunity

Keila Stark
Ecological communities are jointly structured by dispersal, density-independent responses to environmental conditions and density-dependent biotic interactions. Metacommunity ecology provides a framework for understanding how these processes combine to determine community seagrass meadows along the British Columbia coast, we tested the hypothesis that eelgrass (Zostera marina L.) epifaunal invertebrate assemblages are influenced by local environmental conditions, but that high dispersal rates at larger spatial scales dampen effects of environmental differences. We used hierarchical joint species distribution...

Multigene phylogenetics of euglenids based on single-cell transcriptomics of diverse phagotrophs

Gordon Lax, Martin Kolisko, Yana Eglit, Won Je Lee, Naoji Yubuki, Anna Karnkowska, Leander Brian, Gertraud Burger, Patrick Keeling & Alastair Simpson
Euglenids are a well-known group of single-celled eukaryotes, with phototrophic, osmotrophic and phagotrophic members. Phagotrophs represent most of the phylogenetic diversity of euglenids, and gave rise to the phototrophs and osmotrophs, but their evolutionary relationships are poorly understood. Symbiontids, in contrast, are anaerobes that are alternatively inferred to be derived euglenids, or a separate euglenozoan group. Most phylogenetic studies of euglenids have examined the SSU rDNA gene only, which is often highly divergent. Also, many...

Globally, plant-soil feedbacks are weak predictors of plant abundance

Kurt Reinhart, Jonathan Bauer, Sarah McCarthy-Neumann, Andrew MacDougall, José Hierro, Mariana Chiuffo, Scott Mangan, Johannes Heinze, Joana Bergmann, Jasmin Joshi, Richard Duncan, Jeff Diaz, Paul Kardol, Gemma Rutten, Markus Fischer, Wim Van Der Putten, T. Bezemer & John Klironomos
Plant-soil feedbacks (PSFs) have been shown to strongly affect plant performance under controlled conditions, and PSFs are thought to have far reaching consequences for plant population dynamics and the structuring of plant communities. However, thus far the relationship between PSF and plant species abundance in the field is not consistent. Here, we synthesize PSF experiments from tropical forests to semiarid grasslands, and test for a positive relationship between plant abundance in the field and PSFs...

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  • University of British Columbia
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