76 Works

Ancestral reconstruction of sunflower karyotypes reveals non-random chromosomal evolution

Kate Ostevik, Kieran Samuk & Loren Rieseberg
Mapping the chromosomal rearrangements between species can inform our understanding of genome evolution, reproductive isolation, and speciation. Here we present a novel algorithm for identifying regions of synteny in pairs of genetic maps, which is implemented in the accompanying R package, syntR. The syntR algorithm performs as well as previous methods while being systematic and repeatable and can be used to map chromosomal rearrangements in any group of species. In addition, we present a systematic...

Landscape context mediates the physiological stress response of birds to farmland diversification

Christopher Latimer, Olivia Smith, Joseph Taylor, Amanda Edworthy, Jeb Owen, William Snyder & Christina M. Kennedy
1. Farmland diversification practices are increasingly adopted to help reverse biodiversity declines in agroecosystems. However, evidence for the effectiveness of this approach often comes from documenting the species attracted to particular farming systems or landscapes, rather than their underlying physiological states that ultimately determine population growth or decline over the longer term. 2. Across 38 organic, mixed-produce farms spanning the U.S. west coast, we quantified three physiological biomarkers that are widely used to capture variation...

Supplementary materials: Monitoring recovery of overgrazed lichen communities on Hagemeister Island, southwestern Alaska

Patrick Walsh & Trevor Goward
Understanding the recovery rate of overgrazed lichen communities has value to mangers of lands in northern regions. We describe lichen community composition and present recovery rate measurements for a 12-year period following overgrazing by reindeer (Rangifer tarandus) on Hagemeister Island, Alaska. Reindeer were removed from the island in 1993 following overgrazing and average total lichen biomass increased from 504.2 kg/ha (SD 205.4) in 2003 to 795.3 (SD 489.6) in 2015. We estimate time to recovery...

Data from: Thermal tolerances and species interactions determine the elevational distributions of insects

Sarah Amundrud & Diane Srivastava
Aim: While physiological limits to thermal extremes are often thought to determine the abundance and geographic distribution of species, more recent evidence suggests that species interactions may be equally important. Moreover, the relative importance of these constraints may shift with changing abiotic conditions, such as climate change. Here, we explore the relative importance of physiological tolerances to heat and species interactions in determining the distribution of insects along two elevational gradients. The gradients contrast in...

Data from: Divergence of Arctic shrub growth associated with sea ice decline

Agata Buchwal, Patrick F. Sullivan, Marc Macias-Fauria, Eric Post, Isla H. Myers-Smith, Julienne C. Stroeve, Daan Blok, Ken D. Tape, Bruce C. Forbes, Pascale Ropars, Esther Lévesque, Bo Elberling, Sandra Angers-Blondin, Joseph S. Boyle, Stéphane Boudreau, Noémie Boulanger-Lapointe, Cassandra Gamm, Martin Hallinger, Grzegorz Rachlewicz, Amanda Young, Pentti Zetterberg & Jeffrey M. Welker
Arctic sea ice extent (SIE) is declining at an accelerating rate with a wide range of ecological consequences. However, determining sea ice effects on tundra vegetation remains a challenge. In this study, we examined the universality or lack thereof in tundra shrub growth responses to changes in SIE and summer climate across the Pan-Arctic, taking advantage of 23 tundra shrub-ring chronologies from 19 widely distributed sites (56⁰-83⁰N).

Selection on a small genomic region underpins differentiation in multiple color traits between two warbler species

Silu Wang, Sievert Rohwer, Devin De Zwaan, David Toews, Irby Lovette, Jacqueline Mackenzie & Darren Irwin
Speciation is one of the most important processes in biology, yet the study of the genomic changes underlying this process is in its infancy. North American warbler species Setophaga townsendi and S. occidentalis hybridize in a stable hybrid zone, following a period of geographic separation. Genomic differentiation accumulated during geographic isolation can be homogenized by introgression at secondary contact, while genetic regions that cause low hybrid fitness can be shielded from such introgression. Here we...

Temporal instability of lake charr phenotypes: Synchronicity of growth rates and morphology linked to environmental variables?

Louise Chavarie
Pathways through which phenotypic variation among individuals arise can be complex. One assumption often made in relation to intraspecific diversity is that the stability or predictability of the environment will interact with expression of the underlying phenotypic variation. To address biological complexity below the species level, we investigated variability across years in morphology and annual growth increments between and within two sympatric lake charr Salvelinus namaycush ecotypes in Rush Lake, USA. A rapid phenotypic shift...

Five-years of ocrelizumab in relapsing multiple sclerosis: OPERA studies open-label extension

Stephen L Hauser, Ludwig Kappos, Douglas L Arnold, Amit Bar-Or, Bruno Brochet, Robert T Naismith, Anthony Traboulsee, Jerry S Wolinsky, Shibeshih Belachew, Harold Koendgen, Victoria Levesque, Marianna Manfrini, Fabian Model, Stanislas Hubeaux, Lahar Mehta & Xavier Montalban
Objective To assess over 3 years of follow-up, the effects of maintaining or switching to ocrelizumab (OCR) therapy on clinical and MRI outcomes and safety measures in the open-label extension (OLE) phase of the pooled OPERA studies in relapsing multiple sclerosis. Methods After 2 years of double-blind, controlled treatment, patients continued OCR (600 mg infusions every 24 weeks) or switched from interferon (IFN) β-1a (44 μg 3 times weekly) to OCR when entering the OLE...

Organic Carbon at Land-Ocean Interface - Calvert Island - 2014-2016

Kyra St Pierre
This data package includes three datasets used to assess spatial and temporal patterns in dissolved organic carbon (DOC) and particulate organic carbon (POC) across freshwater streams and nearshore marine stations on Calvert and Hecate Islands on British Columbia’s Central Coast, associated with St. Pierre and Oliver et al. (2020, submitted). The datasets include: ‘Compiled Freshwater - Marine Dataset - Final.xlsx’: DOC and POC concentrations and stable isotope signatures across freshwater (n = 7), marine outlet-adjacent...

Data from: Automatic segmentation of multiple cardiovascular structures from cardiac computed tomography angiography images using deep learning

Lohendran Baskaran, Subhi J. Al’Aref, Gabriel Maliakal, Benjamin C. Lee, Zhuoran Xu, Jeong W. Choi, Sang-Eun Lee, Ji Min Sung, Fay Y. Lin, Simon Dunham, Bobak Mosadegh, Yong-Jin Kim, Ilan Gottlieb, Byoung Kwon Lee, Eun Ju Chun, Filippo Cademartiri, Erica Maffei, Hugo Marques, Sanghoon Shin, Jung Hyun Choi, Kavitha Chinnaiyan, Martin Hadamitzky, Edoardo Conte, Daniele Andreini, Gianluca Pontone … & Leslee J. Shaw
Objectives: To develop, demonstrate and evaluate an automated deep learning method for multiple cardiovascular structure segmentation. Background: Segmentation of cardiovascular images is resource-intensive. We design an automated deep learning method for the segmentation of multiple structures from Coronary Computed Tomography Angiography (CCTA) images. Methods: Images from a multicenter registry of patients that underwent clinically-indicated CCTA were used. The proximal ascending and descending aorta (PAA, DA), superior and inferior vena cavae (SVC, IVC), pulmonary artery (PA),...

Data from: A stochastic model for predicting age and mass at maturity of insects

Geoffrey Legault & Joel Kingsolver
Variation in age and mass at maturity is commonly observed in populations, even among individuals with the same genetic and environmental backgrounds. Accounting for such individual variation with a stochastic model is important for estimating optimal evolutionary strategies and for understanding potential trade-offs among life history traits. However, most studies employ stochastic models that are either phenomenological or account for variation in only one life history trait. We propose a model based on the developmental...

Extinction dynamics under extreme conservation threat: the flora of St Helena

Quentin Cronk & Phil Lambdon
The flora of the island of St Helena provides an amplified system for the study of extinction by reason of the island’s high endemism, small size, vulnerable biota, length of time of severe disturbance (since 1502) and severity of threats. Endemic plants have been eliminated from 96.5% of St Helena by habitat loss. There are eight recorded extinctions in the vascular flora since 1771 giving an extinction rate of 581 extinctions per million species per...

Boreal predator co-occurrences reveal shared use of seismic lines in a working landscape

Erin R. Tattersall, Joanna M. Burgar, Jason T. Fisher & A. Cole Burton
Interspecific interactions are an integral aspect of ecosystem functioning that may be disrupted in an increasingly anthropocentric world. Industrial landscape change creates a novel playing field on which these interactions take place, and a key question for wildlife managers is whether and how species are able to coexist in such working landscapes. Using camera traps deployed in northern Alberta, we surveyed boreal predators to determine whether interspecific interactions affected occurrences of black bears (Ursus americanus),...

Molecular assays to detect the presence and viability of Phytophthora ramorum and Grosmannia clavigera

Nicolas Feau, Barbara Wong & Richard Hamelin
Protocols for the RNA and DNA extractions, cDNA synthesis and qPCR and RT-qPCR for detecting and assessing viability of the Phytophthora ramorum and Grosmannia clavigera tree pathogens.

Genomic differentiation and local adaptation on a microgeographic scale in a resident songbird

Jennifer Walsh, Stepfanie Aguillon, Yvonne Chan, Peter Arcese, Phred Benham, Irby Lovette & Chloe Mikles
Elucidating forces capable of driving species diversification in the face of gene flow remains a key goal in evolutionary biology. Song sparrows, Melospiza melodia, occur as 25 subspecies in diverse habitats across North America, are among the continent’s most widespread vertebrate species, and are exemplary of many highly variable species for which the conservation of locally adapted populations may be critical to their range-wide persistence. We focus here on six morphologically distinct subspecies resident in...

Multivariate phenotypic divergence along an urbanization gradient

James Santangelo, L. Rivkin Ruth, Carole Advenard & Ken Thompson
A growing body of evidence suggests that natural populations can evolve to better tolerate the novel environmental conditions associated with urban areas. Invariably, studies of adaptive divergence in urban areas examine only one or a few traits at a time from populations residing only at the most extreme urban and nonurban habitats. Thus, whether urbanization is driving divergence in many traits simultaneously in a manner that varies with the degree of urbanization remains unclear. To...

Data from: A meta-analysis of global avian survival across species and latitude

Micah Scholer, Matt Strimas-Mackey & Jill Jankowski
Tropical birds are thought to be longer lived than many temperate species. We explored the idea of higher survival at tropical latitudes and whether extrinsic climate factors and intrinsic traits helped explain this pattern using a meta-analytical approach. The dataset consists of 949 estimates from 204 studies of avian survival from both New World and Old World biogeographical realms.

Data from: Using genetic relatedness to understand heterogeneous distributions of urban rat-associated pathogens

Kaylee Byers, Tom Booker, Matthew Combs, Chelsea Himsworth, Jason Munshi-South, David Patrick & Michael Whitlock
Urban Norway rats (Rattus norvegicus) carry several pathogens transmissible to people. However, pathogen prevalence can vary across fine spatial scales (i.e., by city block). Using a population genomics approach, we sought to describe rat movement patterns across an urban landscape, and to evaluate whether these patterns align with pathogen distributions. We genotyped 605 rats from a single neighborhood in Vancouver, Canada and used 1,495 genome-wide single nucleotide polymorphisms to identify parent-offspring and sibling relationships using...

Comparative gene expression analysis reveals mechanism of Pinus contorta response to the fungal pathogen Dothistroma septosporum

Mengmeng Lu, Nicolas Feau, Dragana Obreht Vidakovic, Nicholas Ukrainetz, Barbara Wong, Sally Aitken, Richard Hamelin & Sam Yeaman
Many conifers have distributions that span wide ranges in both biotic and abiotic conditions, but the basis of response to biotic stress has received much less attention than response to abiotic stress. In this study, we investigated the gene expression response of lodgepole pine (Pinus contorta) to attack by the fungal pathogen Dothistroma septosporum, which causes Dothistroma needle blight (DNB), a disease that has caused severe climate-related outbreaks in northwestern British Columbia. We inoculated tolerant...

Genetic variation at the species and population levels in the Rocky Mountain ridged mussel (Gonidea angulata) – Supplementary Material

James Walton, Karen E. Mock, Steven Brownlee, Jon H. Mageroy, Greg Wilson & Ian Walker
Freshwater mussels in western North America are threatened by water diversions, climate change, loss of required host fish, and other factors, and have experienced marked decline in the past several decades. All four of the primary lineages (potentially species) of freshwater mussels in the western U.S. and Canada are widespread and have somewhat generalist host fish requirements. Of these lineages, perhaps the most poorly understood and of greatest conservation concern is Gonidea angulata (Rocky Mountain...

Data from: Climate change increases predation risk for a keystone species of the boreal forest

Michael Peers, Yasmine Majchrzak, Allyson Menzies, Emily Studd, Guillaume Bastille-Rousseau, Rudy Boonstra, Murray Humphries, Thomas Jung, Alice Kenney, Charles Krebs, Dennis Murray & Stan Boutin
Canada lynx (Lynx canadensis) and snowshoe hares (Lepus americanus) form a keystone predator-prey cycle that has large impacts on the North-American boreal forest vertebrate community. Snowshoe hares and lynx are both well-suited for snowy winters, but climate change associated shifts in snow conditions could lower hare survival and alter cyclic dynamics. Using detailed monitoring of snowshoe hare cause-specific mortality, behaviour, and prevailing weather, we demonstrate that hare mortality risk is strongly influenced by variation in...

Multiple chromosomal inversions contribute to adaptive divergence of a dune sunflower ecotype

Kaichi Huang, Rose Andrew, Gregory Owens, Katherine Ostevik & Loren Rieseberg
Both models and case studies suggest that chromosomal inversions can facilitate adaptation and speciation in the presence of gene flow by suppressing recombination between locally adapted alleles. Until recently, however, it has been laborious and time-consuming to identify and genotype inversions in natural populations. Here we apply RAD sequencing data and newly developed population genomic approaches to identify putative inversions that differentiate a sand dune ecotype of the prairie sunflower (Helianthus petiolaris) from populations found...

Global gradients in intraspecific variation in vegetative and floral traits are partially associated with climate and species richness

Jonas Kuppler, Cécile H. Albert, Gregory M. Ames, W. Scott Armbruster, Gerhard Boenisch, Florian C. Boucher, Diane R. Campbell, Liedson T. Carneiro, Eduardo Chacón-Madrigal, Brian J. Enquist, Carlos R. Fonseca, José M. Gómez, Antoine Guisan, Pedro Higuchi, Dirk N. Karger, Jens Kattge, Michael Kleyer, Nathan J. B. Kraft, Anne-Amélie C. Larue-Kontić, Amparo Lázaro, Martin Lechleitner, Deirdre Loughnan, Vanessa Minden, Ülo Niinemets, Gerhard E. Overbeck … & Robert R. Junker
Aim Intraspecific trait variation (ITV) within natural plant communities can be large, influencing local ecological processes and dynamics. Here, we shed light on how ITV in vegetative and floral traits responds to large-scale abiotic and biotic gradients (i.e. climate and species richness). Specifically, we tested if associations of ITV with temperature, precipitation and species richness were consistent with any of from four hypotheses relating to stress-tolerance and competition. Furthermore, we estimated the degree of correlation...

Data from: Prey availability and ambient temperature influence carrion persistence in the boreal forest

Michael Peers, Sean Konkolics, Clayton Lamb, Yasmine Majchrzak, Allyson Menzies, Emily Studd, Rudy Boonstra, Alice Kenney, Charles Krebs, April Robin Martinig, Baily McCulloch, Joseph Silva, Laura Garland & Stan Boutin
1. Scavenging by vertebrates can have important impacts on food web stability and persistence, and can alter the distribution of nutrients throughout the landscape. However, scavenging communities have been understudied in most regions around the globe, and we lack understanding of the biotic drivers of vertebrate scavenging dynamics. 2. In this paper, we examined how changes in prey density and carrion biomass caused by population cycles of a primary prey species, the snowshoe hare (Lepus...

Data from: The function and evolution of motile DNA replication systems in ciliates

Nicholas Irwin, Alexandros Pittis, Varsha Mathur, LeAnn Howe, Patrick Keeling, Denis Lynn & William Bourland
DNA replication is a ubiquitous, complex, and conserved cellular process. However, regulation of DNA replication is only understood in a small fraction of organisms that poorly represent the diversity of genetic systems in nature. Here we used a combination of computational and experimental approaches to examine the function and evolution of one such system, the replication band (RB) in spirotrich ciliates, which is a localized, motile hub that traverses the macronucleus while replicating DNA. We...

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  • 2020
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Affiliations

  • University of British Columbia
    76
  • Duke University
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  • University of Alberta
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  • McGill University
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  • University of Toronto
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  • University of California, Berkeley
    3
  • University of California, Davis
    3
  • University of Washington
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  • The Nature Conservancy
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  • University of Georgia
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