183 Works

Bacterial dispersal and drift drive microbiome diversity patterns within a population of feral hindgut fermenters

Mason Stothart, Ruth Greuel, Stefan Gavriliuc, Astrid Henry, Alastair Wilson, Philip McLoughlin & Jocelyn Poissant
Studies of microbiome variation in wildlife often emphasize host physiology and diet as proximate selective pressures acting on host-associated microbiota. In contrast, microbial dispersal and ecological drift are more rarely considered. Using amplicon sequencing, we characterized the bacterial microbiome of adult female (n = 86) Sable Island horses (Nova Scotia, Canada) as part of a detailed individual-based study of this feral population. Using data on sampling date, horse location, age, parental status, and local habitat...

Supplementary references from: Thrombus composition, imaging, and outcome prediction in acute ischemic stroke

Bijoy Menon & Raed Joundi
Purpose of the Review: This article reviews the biochemical, structural, and imaging characteristics of intracranial thrombi in acute ischemic stroke; the relationship between thrombus composition and response to lytic and endovascular therapies; and current and future directions for improving outcomes in acute stroke patients based on thrombus characteristics. Recent Findings: New imaging techniques have advanced our ability to capture thrombus characteristics and burden in real-time, An improved understanding of recanalization rates with thrombolysis and endovascular...

Hemotological and morphometric measurements from geladas

Kenneth L. Chiou, Mareike C. Janiak, India A. Schneider-Crease, Sharmi Sen, Ferehiwot Ayele, Idrissa S. Chuma, Sascha Knauf, Alemayehu Lemma, Anthony V. Signore, Anthony M. D’Ippolito, Belayneh Abebe, Abebaw Azanaw Haile, Fanuel Kebede, Peter J. Fashing, Nga Nguyen, Colleen McCann, Marlys L. Houck, Jeffrey D. Wall, Andrew S. Burrell, Christina M. Bergey, Jeffrey Rogers, Jane E. Phillips-Conroy, Clifford J. Jolly, Amanda D. Melin, Jay F. Storz … & Noah Snyder-Mackler
Primates have adapted to numerous environments and lifestyles but very few species are native to high elevations. Here, we investigated high-altitude adaptations in the gelada (Theropithecus gelada), a monkey endemic to the Ethiopian Plateau. We examined genome-wide variation in conjunction with measurements of haematological and morphological traits. Our new gelada reference genome is highly intact and assembled at chromosome-length levels. Unexpectedly, we identified a chromosomal polymorphism in geladas that could potentially contribute to reproductive barriers...

Decline effects are rare in ecology: a meta-meta-analysis

Jeremy Fox & Laura Costello
The scientific evidence base on any given topic changes over time as more studies are published. Currently, there is widespread concern about non-random, directional changes over time in the scientific evidence base associated with many topics. In particular, if studies finding large effects (e.g., large differences between treatment and control means) tend to get published quickly, while small effect sizes tend to get published slowly, the net result will be a decrease over time in...

Evolution of thermal physiology alters the projected range of threespine stickleback under climate change

Sara Wuitchik, Stephanie Mogensen, Tegan Barry, Antoine Paccard, Heather Jamniczky, Rowan Barrett & Sean Rogers
Species distribution models (SDMs) are widely used to predict range shifts but could be unreliable under climate change scenarios because they do not account for evolution. The thermal physiology of a species is a key determinant of range and thus incorporating thermal trait evolution into SDMs might be expected to alter projected ranges. We identified a genetic basis for physiological and behavioural traits that evolve in response to temperature change in natural populations of threespine...

Association between physical activity and mortality among community-dwelling stroke survivors

Raed Joundi
Objective: To determine the relationship between physical activity and mortality in community-dwelling stroke survivors. Methods: The Canadian Community Health Survey was used to obtain self-reported physical activity (PA) across four survey years and was linked to administrative databases to obtain prior diagnosis of stroke and subsequent all-cause mortality. PA was measured as metabolic equivalents (METs) per week and meeting minimal PA guidelines was defined as 10 MET-hours/week. Cox proportional hazard regression models and restricted cubic...

3D images of a turtle embryo

Yuzheng Ke, Rui Wu, Darla Zelenitsky, Don Brinkman, Jinfeng Hu, Shukang Zhang, Haishui Jiang & Fenglu Han
Turtle eggs containing embryos are exceedingly rare in the fossil record. Here, we provide the first description and taxonomic identification, to our knowledge, of a fossilized embryonic turtle preserved in an egg, a fossil recovered from the Upper Cretaceous Xiaguan Formation of Henan Province, China. Through Computed Tomography and Three-Dimensional reconstruction, many bones can be clearly displayed, including the maxillae, mandibles, ribs, plastral plates, scapula, forelimbs, and hind limbs. The specimen is attributed to the...

Data from: Targeted genome-wide SNP genotyping in feral horses using non-invasive fecal swabs

Stefan Gavriliuc, Salman Reza, Chanwoori Jeong, Philip McLoughlin & Jocelyn Poissant
The development of high-throughput sequencing has prompted a transition in wildlife genetics from using microsatellites toward sets of Single Nucleotide Polymorphisms (SNPs). However, genotyping large numbers of targeted SNPs using non-invasive samples remains challenging due to relatively large DNA input requirements. Recently, target enrichment has emerged as a promising approach requiring little template DNA. We assessed the efficacy of Tecan Genomics’ Allegro Targeted Genotyping (ATG) for generating genome-wide SNP data in feral horses using DNA...

Data from: Modularity of genes involved in local adaptation to climate despite physical linkage

Katie E. Lotterhos, Sam Yeaman, Jon Degner, Sally Aitken & Kathryn A. Hodgins
Background: Linkage among genes experiencing different selection pressures can make natural selection less efficient. Theory predicts that when local adaptation is driven by complex and non-covarying stresses, increased linkage is favored for alleles with similar pleiotropic effects, with increased recombination favored among alleles with contrasting pleiotropic effects. Here, we introduce a framework to test these predictions with a co-association network analysis, which clusters loci based on differing associations. We use this framework to study the...

Shallow shotgun sequencing of the microbiome recapitulates 16S amplicon results and provides functional insights

Mason Stothart, Philip McLoughlin & Jocelyn Poissant
Prevailing 16S rRNA gene-amplicon methods for characterizing the bacterial microbiome of wildlife are economical, but result in coarse taxonomic classifications, are subject to primer and 16S copy number biases, and do not allow for direct estimation of microbiome functional potential. While deep shotgun metagenomic sequencing can overcome many of these limitations, it is prohibitively expensive for large sample sets. We evaluated the ability of shallow shotgun metagenomic sequencing to characterize taxonomic and functional patterns in...

Mt. Meager Geothermal Nodal Array

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Numerous hot springs dot the Garibaldi Volcanic Belt, in southwestern British Columbia. This is a zone of recent volcanism in the northernmost segment of the Cascade Arc. The source of this geothermal heat, and how it connects to the surrounding volcanic belt serves as the focus of a temporary seismic deployment of 59 earthquake monitoring stations during the summer and fall of 2019. These instruments are comprised of Inova Hawk nodal systems connected to 10...

Data from: The design of a beautiful weapon: compensation for opposing sexual selection on a trait with two functions

Stefan Dennenmoser & John H. Christy
Male fiddler crabs, genus Uca, have one greatly enlarged claw with which they court females and threaten and fight other males. Longer claws are more effective signals but are thought to be less effective weapons because the relative closing force at the tip of the claw decreases with claw length. We studied claw morphology and fighting in Uca terpsichores and Uca beebei and found a mechanism that may resolve opposing selection for signaling and fighting...

Data from: Discovery of metabolic biomarkers for Duchenne Muscular Dystrophy within a natural history study

Simina M. Boca, Maki Nishida, Michael Harris, Shruti Rao, Amrita K. Cheema, Kirandeep Gill, Haeri Seol, Lauren P. Morgenroth, Erik Henricson, Craig McDonald, Jean K. Mah, Paula R. Clemens, Eric P. Hoffman, Yetrib Hathout & Subha Madhavan
Serum metabolite profiling in Duchenne muscular dystrophy (DMD) may enable discovery of valuable molecular markers for disease progression and treatment response. Serum samples from 51 DMD patients from a natural history study and 22 age-matched healthy volunteers were profiled using liquid chromatography coupled to mass spectrometry (LC-MS) for discovery of novel circulating serum metabolites associated with DMD. Fourteen metabolites were found significantly altered (1% false discovery rate) in their levels between DMD patients and healthy...

Data from: Transcriptome dynamics over a lunar month in a broadcast spawning Acroporid coral

Matthew J. Oldach, Matthew Workentine, Mikhail V. Matz, Tung-Yung Fan & Peter D. Vize
On one night per year, at a specific point in the lunar cycle, one of the most extraordinary reproductive events on the planet unfolds as hundreds of millions of broadcast spawning corals release their trillions of gametes into the waters of the tropical seas. Each species spawns on a specific night within the lunar cycle, typically from full moon to third quarter moon, and in a specific time window after sunset. This accuracy is essential...

Data from: Growth gains from selective breeding in a spruce hybrid zone do not compromise local adaptation to climate

Ian R. MacLachlan, Sam Yeaman & Sally N. Aitken
Hybrid zones contain extensive standing genetic variation that facilitates rapid responses to selection. The Picea glauca x P. engelmannii hybrid zone in western Canada is the focus of tree breeding programs that annually produce ~90 million reforestation seedlings. Understanding the direct and indirect effects of selective breeding on adaptive variation is necessary to implement assisted gene flow polices in Alberta and British Columbia that match these seedlings with future climates. We decomposed relationships among hybrid...

Data from: Phylogenetic tree shape and the structure of mutualistic networks

Scott Chamberlain, Diego P. Vázquez, Luisa Carvalheiro, Elizabeth Elle & Jana C. Vamosi
Species community composition is known to alter the network of interactions between two trophic levels, potentially affecting its functioning (e.g. plant pollination success) and the stability of communities. Phylogenies vary in shape with regard to the rate of evolutionary change across a tree (influencing tree balance) and variation in the timing of branching events (affecting the distribution of node ages in trees), both of which may influence the structure of species interaction networks. Because related...

Data from: Species traits and abundances predict metrics of plant–pollinator network structure, but not pairwise interactions

Colin Olito & Jeremy W. Fox
Plant–pollinator mutualistic networks represent the ecological context of foraging (for pollinators) and reproduction (for plants and some pollinators). Plant–pollinator visitation networks exhibit highly conserved structural properties across diverse habitats and species assemblages. The most successful hypotheses to explain these network properties are the neutrality and biological constraints hypotheses, which posit that species interaction frequencies can be explained by species relative abundances, and trait mismatches between potential mutualists respectively. However, previous network analyses emphasize the prediction...

Data from: Best practices for justifying fossil calibrations

James F. Parham, Philip C. J. Donoghue, Christopher J. Bell, Tyler D. Calway, Jason J. Head, Patricia A. Holroyd, Jun G. Inoue, Randall B. Irmis, Walter G. Joyce, Daniel T. Ksepka, José S. L. Patané, Nathan D. Smith, James E. Tarver, Marcel Van Tuinen, Ziheng Yang, Kenneth D. Angielczyk, Jenny M. Greenwood, Christy A. Hipsley, Jacobs Louis, Peter J. Makovicky, Johannes Müller, Krister T. Smith, Jessica M. Theodor, Rachel C. M. Warnock, Michael J. Benton … & Louis Jacobs
Our ability to correlate biological evolution with climate change, geological evolution, and other historical patterns is essential to understanding the processes that shape biodiversity. Combining data from the fossil record with molecular phylogenetics represents an exciting synthetic approach to this challenge. The first molecular divergence dating analysis (Zuckerkandl and Pauling 1962) was based on a measure of the amino acid differences in the hemoglobin molecule; with replacement rates established (calibrated) using inaccurate paleontological age estimates...

Commodity canola insect visitation

Samuel Robinson, Shelley Hoover, Stephen Pernal & Ralph Cartar
These data were used in a simulation study to examine how honey bees distribute themselves across foraging landscapes. The ideal-free distribution and central-place foraging are important ecological models that can explain the distribution of foraging organisms in their environment. However, this model ignores distance-based foraging costs from a central place (hive, nest), while central-place foraging ignores competition. Different foraging currencies and cooperation between foragers also create different optimal distributions of foragers, but are limited to...

High-frequency measurements of aeolian saltation flux: time series data

Raleigh L. Martin, Jasper F. Kok, Chris H. Hugenholtz, Thomas E. Barchyn, Marcelo Chamecki & Jean T. Ellis
High-frequency (25-50 Hz) coupled observations of wind speed and aeolian saltation flux (i.e, the wind-blown movement of sand) were measured at three field sites: Jericoacoara, Brazil; Rancho Guadalupe, California; and Oceano, California. The dataset provided here contains the full record of raw and processed time series of saltation flux and wind speed measured at multiple heights above the sediment surface.

Geography, seasonality, and host‐associated population structure influence the fecal microbiome of a genetically depauparate Arctic mammal

Samantha Bird, Erin Prewer, Susan Kutz, Lisa-Marie Leclerc, Sibelle T. Vilaça & Christopher J. Kyle
The Canadian Arctic is an extreme environment with low floral and faunal diversity characterized by major seasonal shifts in temperature, moisture and daylight. Muskoxen (Ovibos moschatus) are one of few large herbivores able to survive this harsh environment. Microbiome research of the gastrointestinal tract may hold clues as to how muskoxen exist in the Arctic, but also how this species may respond to rapid environmental changes. In this study, we investigated the effects of season...

Gene clustering and copy number variation in alkaloid metabolic pathways of opium poppy

Qiushi Li, Sukanya Ramasamy, Pooja Singh, Jillian Hagel, Sonja Dunemann, Xue Chen, Rongji Chen, Lisa Yu, Joseph Tucker, Peter Facchini & Sam Yeaman
Genes in plant secondary metabolic pathways enable the biosynthesis of a range of medically and industrially important compounds, and are often clustered on chromosomes. Here, we study genomic clustering in the benzylisoquinoline alkaloid (BIA) pathway in opium poppy (Papaver somniferum), exploring relationships between gene expression, copy number variation, and metabolite production. We use Hi-C to improve the existing draft genome assembly, yielding chromosome-scale scaffolds that include 35 previously unanchored BIA genes. We find that co-expression...

Data from: The role of nocturnal omnivorous lemurs as seed dispersers in Malagasy rain forests

Veronarindra Ramananjato, Zafimahery Rakotomalala, Daniel S. Park, Camille M. M. DeSisto, Nancia N. Raoelinjanakolona, Nicola K. Guthrie, Zo E. S. Fenosoa, Steig E. Johnson & Onja H. Razafindratsima
Fruit-eating animals play important roles as seed dispersal agents in terrestrial systems. Yet, the extent to which seed dispersal by nocturnal omnivores may facilitate germination and the recruitment of plant communities has rarely been investigated. Characterizing their roles in seed dispersal is necessary to provide a more complete picture of how seed dispersal processes affect ecosystem functioning. We investigated the roles and impacts of two species of nocturnal omnivorous lemur species, Microcebus jollyae and M....

Experimental evolution of competing bean beetle species reveals long-term reversals of short-term evolution, but no consistent character displacement

Jeremy Fox, Stephen Hausch & Steven Vamosi
Interspecific competition for shared resources should select for evolutionary divergence in resource use between competing species, termed character displacement. Many purported examples of character displacement exist, but few completely rule out alternative explanations. We reared genetically-diverse populations of two species of bean beetles, Callosobruchus maculatus and C. chinensis, in allopatry and sympatry on a mixture of adzuki beans and lentils, and assayed oviposition preference and other phenotypic traits after four, eight, and twelve generations of...

The evolution of startle displays: a case study in praying mantises

Marta Vidal-Garcia, James C. O’Hanlon, Gavin J. Svenson & Kate D. L. Umbers
Anti-predator defences are typically regarded as static signals that conceal prey or advertise their unprofitability. However, startle displays are performed by prey when attacked and can include a spectacular array of movements, colours, and sounds. Here we present the first phylogenetically-controlled comparative analyses of startle displays including behaviour, using praying mantises as a test case. For 58 species, with a dated phylogeny, we estimate the strength of phylogenetic signal in the presence and ‘complexity’ (number...

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