23 Works

Limited genetic parallelism underlies recent, repeated incipient speciation in geographically proximate populations of an Arctic fish (Salvelinus alpinus)

Sarah J. Salisbury, Gregory R. McCracken, Robert Perry, Donald Keefe, Kara K. S. Layton, Tony Kess, Cameron M. Nugent, Jong S. Leong, Ian R. Bradbury, Ben F. Koop, Moira M. Ferguson & Daniel E. Ruzzante
The genetic underpinnings of incipient speciation, including the genomic mechanisms which contribute to morphological and ecological differentiation and reproductive isolation, remain poorly understood. The repeated evolution of consistently, phenotypically distinct morphs of Arctic Charr (Salvelinus alpinus) within the Quaternary period offer an ideal model to study the repeatability of evolution at the genomic level. Sympatric morphs of Arctic Charr are found across this species' circumpolar distribution. However, the specific genetic mechanisms driving this morph differentiation...

Data from: Molecular underpinnings and biogeochemical consequences of enhanced diatom growth in a warming Southern Ocean

Loay Jabre, Andrew E. Allen, J. Scott P. McCain, John P. McCrow, Nancy Tenenbaum, Jenna L. Spackeen, Rachel E. Sipler, Beverley R. Green, Deborah A. Bronk, David A. Hutchins & Erin M. Bertrand
The Southern Ocean (SO) harbours some of the most intense phytoplankton blooms on Earth. Changes in temperature and iron availability are expected to alter the intensity of SO phytoplankton blooms, but little is known about how environmental change will influence community composition and downstream biogeochemical processes. We performed experimental manipulations on surface ocean microbial communities from McMurdo Sound in the Ross Sea, with and without iron addition, at -0.5 °C, 3 °C, and 6 °C....

Temperature-dependent effects of sea-louse infestation on juvenile Atlantic salmon

Sean Godwin
Infectious diseases are key drivers of wildlife populations and agriculture production, but whether and how climate change will influence disease impacts remains controversial. One of the critical knowledge gaps that prevents resolution of this controversy is a lack of high-quality experimental data, especially in marine systems of significant ecological and economic consequence. Here, we performed a manipulative experiment in which we tested the temperature-dependent effects on Atlantic salmon (Salmo salar) of sea lice (Lepeophtheirus salmonis)...

Multiple drainage reversal episodes and glacial refugia in a Patagonian fish revealed by sequenced microsatellites

Daniel Ruzzante, Annie Simons, Gregory McCracken, Evelyn Habit & Sandra Walde
The rise of the southern Andes and the Quaternary glacial cycles influenced the landscape of Patagonia, affecting the phylogeographic and biogeographic patterns of its flora and fauna. Here we examine the phylogeography of the freshwater fish, Percichthys trucha, using 53 sequenced microsatellite DNA markers. Fish (N=835) were collected from 16 river systems (46 locations) spanning the species range on both sides of the Andes. Eleven watersheds drain to the Pacific, five of which are trans-Andean...

Hippoglossus hippoglossus SNP data for coverage-based sex association

Anthony Einfeldt & Tony Kess
Changes in the genetic mechanisms that control sexual determination have occurred independently across the tree of life, and with exceptional frequency in teleost fishes. To investigate the genomic changes underlying the evolution of sexual determination, we sequenced a chromosome-level genome, multi-tissue transcriptomes, and population genomic data for the Atlantic Halibut (Hippoglossus hippoglossus), which has an XY/XX sex determination mechanism and has recently diverged from the Pacific Halibut (Hippoglossus stenolepis), which has a ZZ/ZW system. We...

Data from: Environmental change, if unaccounted, prevents detection of cryptic evolution in a wild population

Tomos Potter, Ronald D. Bassar, Paul Bentzen, Emily W. Ruell, Julián Torres-Dowdall, Corey A. Handelsman, Cameron K. Ghalambor, Joseph Travis, David N. Reznick & Tim Coulson
Detecting contemporary evolution requires demonstrating that genetic change has occurred. Mixed-effects models allow estimation of quantitative genetic parameters and are widely used to study evolution in wild populations. However, predictions of evolution based on these parameters frequently fail to match observations. Furthermore, such studies often lack an independent measure of evolutionary change against which to verify predictions. Here, we applied three commonly used quantitative genetic approaches to predict the evolution of size at maturity in...

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...

Evolutionary impacts differ between two exploited populations of northern bottlenose whale (Hyperoodon ampullatus)

Anthony Einfeldt, Laura Feyrer, Paul Bentzen, Hal Whitehead & Ian Paterson
Interpretation of conservation status should be informed by an appreciation of genetic diversity, past demography, and overall trends in population size, which contribute to a species’ evolutionary potential and resilience to genetic risks. Low genetic diversity can be symptomatic of rapid demographic declines and impose genetic risks to populations, but can also be maintained by natural processes. The northern bottlenose whale Hyperoodon ampullatus has the lowest known mitochondrial diversity of any cetacean and was intensely...

Cascading effects of climate change on plankton community structure

Grace Murphy, Boris Worm & Tamara Romanuk
Plankton communities account for at least half of global primary production and play a key role in the global carbon cycle. Warming and acidification may alter the interaction chains in these communities from the bottom and top of the food web. Yet, the relative importance of these potentially complex interactions has not yet been quantified. Here we examine the isolated and combined effects of warming, acidification, and reductions in phytoplankton and predator abundances in a...

Screening the Sigma LOPAC®1280 library of compounds for protective effects against cisplatin-induced oto- and nephrotoxicity

Jaime Wertman, Nicole Melong, Matthew Stoyek, Olivia Piccolo, Stewart Langley, Benno Orr, Shelby Steele, Babak Razaghi & Jason Berman
Dose-limiting toxicities for cisplatin administration, including ototoxicity and nephrotoxicity, impact the clinical utility of this effective chemotherapy agent and lead to lifelong complications, particularly in pediatric cancer survivors. Using a two-pronged drug screen employing the zebrafish lateral line as an in vivo readout for ototoxicity and kidney cell-based nephrotoxicity assay, we screened 1280 compounds and identified 22 that were both oto- and nephroprotective. Of these, dopamine and L-mimosine, a plant-based amino acid active in the...

Data from: Latent developmental and evolutionary shapes embedded within the grapevine leaf

Dan Chitwood, Robert VanBuren, Zoë Migicovsky, Margaret Frank & Jason Londo
Across plants, leaves exhibit profound diversity in shape. As a single leaf expands, its shape is in constant flux. Plants may also produce leaves with different shapes at successive nodes. In addition, leaf shape varies among individuals, populations and species as a result of evolutionary processes and environmental influences. Because leaf shape can vary in many different ways, theoretically, the effects of distinct developmental and evolutionary processes are separable, even within the shape of a...

Past and future decline of tropical pelagic biodiversity

Moriaki Yasuhara, Chih-Lin Wei, Michal Kucera, Mark Costello, Derek Tittensor, Wolfgang Kiessling, Timothy Bonebrake, Clay Tabor, Ran Feng, Andrés Baselga, Kerstin Kretschmer, Buntarou Kusumoto & Yasuhiro Kubota
A major research question concerning global pelagic biodiversity remains unanswered: when did the apparent tropical biodiversity depression (i.e., bimodality of latitudinal diversity gradient [LDG]) begin? The bimodal LDG may be a consequence of recent ocean warming or of deep-time evolutionary speciation and extinction processes. Using rich time-slice datasets of planktonic foraminifers, we show here that a unimodal (or only weakly bimodal) diversity gradient, with a plateau in the tropics, occurred during the last ice age...

Data from: Divergent and linked selection shape patterns of genomic differentiation between European and North American Atlantic salmon (Salmo salar)

Sarah Lehnert, Tony Kess, Paul Bentzen, Marie Clément & Ian Bradbury
As populations diverge many processes can shape genomic patterns of differentiation. Regions of high differentiation can arise due to divergent selection acting on selected loci, genetic hitchhiking of nearby loci, or through repeated selection against deleterious alleles (linked background selection); this divergence may then be further elevated in regions of reduced recombination. Atlantic salmon (Salmo salar) from Europe and North America diverged >600,000 years ago and despite some evidence of secondary contact, the majority of...

Data from: Experimental study of species invasion – early population dynamics and role of disturbance in invasion success

David Reznick, Sebastiano De Bona, Andres Lopez-Sepulcre, Mauricio Torres, Ronald Bassar, Paul Bentzen & Joseph Travis
Much of our understanding of natural invasions is retrospective, based on data acquired after invaders become established. As a consequence, we know little about the characteristics of the early population growth and habitat use of the invaders during establishment. Here we report on experimental introductions of guppies into natural streams in which we conducted monthly censuses of each population. Two of the four introductions were in streams with thinned canopies, which mimics a common form...

Interactive Effects of Iron and Temperature on the Growth of Fragilariopsis cylindrus

Loay Jabre & Erin Bertrand
Iron and temperature are important drivers controlling phytoplankton growth in the Southern Ocean. Most studies examining phytoplankton responses to these variables consider them independently, testing responses to changing temperature under constant iron and vice versa. Consequently, we lack a phenomenological and mechanistic understanding of how concurrent changes in these variables influence primary productivity. Here we used a matrix of three temperatures and eight iron levels to examine changes in growth rate, photophysiology and size in...

Multiple decades of stocking has resulted in limited hatchery introgression in wild brook trout (Salvelinus fontinalis) populations of Nova Scotia

Sarah Lehnert, Shauna Baillie, John MacMillan, Ian Paterson, Colin Buhariwalla, Ian Bradbury & Paul Bentzen
Many populations of freshwater fishes are threatened with losses, and increasingly, the release of hatchery individuals is one strategy being implemented to support wild populations. However, stocking of hatchery individuals may pose long-term threats to wild populations, particularly if genetic interactions occur between wild and hatchery individuals. One highly prized sport fish that has been heavily stocked throughout its range is the brook trout (Salvelinus fontinalis). In Nova Scotia, Canada, hatchery brook trout have been...

Prolonged maternal investment in northern bottlenose whales alters our understanding of beaked whale reproductive life history

Laura Feyrer, Shu Ting Zhao, Hal Whitehead & Cory Matthews
Nursing and weaning periods are poorly understood in cetaceans due to the difficulty of assessing underwater behaviour in the wild. However, the onset and completion of weaning are critical turning points for individual development and survival, with implications for a species life history including reproductive potential. δ15N and δ13C deposited in odontocete teeth annuli provide a lifetime record of diet, offering an opportunity to investigate variation and trends in fundamental biology. While available reproductive parameters...

Supplementary material for: Long branch attraction biases in phylogenetics

Edward Susko & Andrew Roger
Long branch attraction is a prevalent form of bias in phylogenetic estimation but the reasons for it are only partially understood. We argue here that it is largely due to differences in the sizes of the model spaces corresponding to different trees. Trees with long branches together allow much more flexible internal branch-length parameter estimation. Consequently, although each tree has the same number of parameters, trees with long branches together have larger effective model spaces....

Resolving fine-scale population structure and fishery exploitation using sequenced microsatellites in a northern fish

Kara K.S. Layton, J. Brian Dempson, Paul V.R. Snelgrove, Steven J. Duffy, Amber M. Messmer, Ian Paterson, Nicholas W. Jeffery, Tony Kess, John B. Horne, Sarah J. Salisbury, Daniel E. Ruzzante, Paul Bentzen, David Côté, Cameron M. Nugent, Moira M. Ferguson, Jong S. Leong, Ben F. Koop & Ian R. Bradbury
The resiliency of populations and species to environmental change is dependent on the maintenance of genetic diversity, and as such quantifying diversity is central to combatting ongoing wide spread reductions in biodiversity. With the advent of next-generation sequencing, several methods now exist for resolving fine-scale population structure, but the comparative performance of these methods for genetic assignment has rarely been tested. Here we evaluate the performance of sequenced microsatellites and a single nucleotide polymorphism (SNP)...

Data from: Understanding families' experiences following a diagnosis of non-syndromic Craniosynostosis: A qualitative study

Victoria Kuta, Lauren Curry, P. Daniel McNeely, Simon Walling, Jill M. Chorney & Michael Bezuhly
Objectives: Craniosynostosis, a congenital anomaly producing an abnormal cranial morphology, is typically diagnosed and surgically corrected within the first year of life. Given the young age of this patient population at the time of diagnosis, it is reasonable to expect this experience to be a very significant and stressful ordeal for patient families. Despite this, there is little research exploring the impact that craniosynostosis has on families, especially in the early stages. In this study,...

Barthelonids represent a deep-branching metamonad clade with mitochondrion-related organelles predicted to generate no ATP

Euki Yazaki, Keitaro Kume, Takashi Shiratori, Yana Eglit, Goro Tanifuji, Ryo Harada, Alastair Simpson, Ken-Ichiro Ishida, Tetsuo Hashimoto & Yuji Inagaki
We here report the phylogenetic position of barthelonids, small anaerobic flagellates previously examined using light microscopy alone. Barthelona spp. were isolated from geographically distinct regions and we established five laboratory strains. Transcriptomic data generated from one Barthelona strain (PAP020) were used for large-scale, multi-gene phylogenetic (phylogenomic) analyses. Our analyses robustly placed strain PAP020 at the base of the Fornicata clade, indicating that barthelonids represent a deep-branching Metamonad clade. Considering the anaerobic/microaerophilic nature of barthelonids and...

rhinoceros auklet microsatellite data

Theresa Burg, Marie Prill, Katharine Studholme, Alice Domalik, Strahan Tucker, Catherine Jardine, Mark Maftei, Kenneth Wright, Jesse Beck, Russell Bradley, Ryan Carle, Thomas Good, Scott Hatch, Peter Hodum, Motohiro Ito, Scott Pearson, Nora Rojek, Leslie Slater, Yutaka Watanuki, Alexis Will, Aidan Bindoff, Glenn Crossin, Mark Drever & Mark Hipfner
We tested the hypothesis that segregation in wintering areas promotes population differentiation in a sentinel North Pacific seabird, the rhinoceros auklet (Cerorhinca monocerata). We collected tissue samples for genetic analyses on five breeding colonies in the western Pacific Ocean (Japan) and 13 in the eastern Pacific Ocean (California to Alaska), and deployed light-level geologgers on 12 eastern Pacific colonies to delineate wintering areas. Loggers were deployed previously on one colony in Japan. There was strong...

The molecular diversity of phagotrophic Euglenids examined using single-cell methods

Gordon Lax & Alastair Simpson
Euglenids are a diverse group of euglenozoan flagellates that includes phototrophs, osmotrophs, andphagotrophs. Despite making up most of the phylogenetic diversity of euglenids, phagotrophs remain understudied, and recent work has focused on ‘deep-branching’ groups. Spirocuta is the large clade encompassing all flexible euglenids including the phototroph and primary osmotroph clades, plus various phagotrophs. Understanding the phylogenetic diversity of phagotrophic spirocutes is crucial for tracing euglenid evolution, including how phototrophs arose.We used single-cell approaches to greatly...

Registration Year

  • 2020

Resource Types

  • Dataset


  • Dalhousie University
  • Fisheries and Oceans Canada
  • University of Guelph
  • National Oceanic and Atmospheric Administration
  • University of California, Riverside
  • University of British Columbia
  • Williams College
  • University of Victoria
  • Florida State University
  • University of Erlangen-Nuremberg