77 Works

Predicting the strength of urban-rural clines in a Mendelian polymorphism along a latitudinal gradient

James Santangelo, Ken Thompson, Beata Cohan, Jibran Syed, Rob Ness & Marc Johnson
Cities are emerging as models for addressing the fundamental question of whether populations evolve in parallel to similar environments. Here, we examine the environmental factors that drive the evolution of parallel urban-rural clines in a Mendelian trait—the cyanogenic antiherbivore defense of white clover (Trifolium repens). Previous work suggested urban-rural gradients in frost and snow depth could drive the evolution of reduced hydrogen cyanide (HCN) frequencies in urban populations. Here, we sampled over 700 urban and...

Parallel flowering time clines in native and introduced ragweed populations are likely due to adaptation

Brechann McGoey, Kathryn Hodgins & John Stinchcombe
As introduced species expand their ranges, they often encounter differences in climate which are often correlated with geography. For introduced species, encountering a geographically variable climate sometimes leads to the re-establishment of clines seen in the native range. However, clines can also be caused by neutral processes, and so it is important to gather additional evidence that population differentiation is the result of selection as opposed to non-adaptive processes. Here, we examine phenotypic and genetic...

Data from: Invasive dominance and resident diversity: unpacking the impact of plant invasion on biodiversity and ecosystem function

Stuart Livingstone, Marney Isaac & Marc Cadotte
Plant invasions have consistently been shown to cause significant reductions in the diversity of recipient plant communities; an effect that can cascade through ecosystems to impact the stocks and flows of nutrients and energy as well as the diversity of higher trophic levels. However, the manner in which invasive plants alter ecosystem functioning and trophic interactions is highly variable can occur through the direct effects of the invader’s abundance and its indirect effects via changes...

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: Paleoclimatic evolution as the main driver of current genomic diversity in the widespread and polymorphic Neotropical songbird Arremon taciturnus

Nelson Buainain, Roberta Canton, Gabriela Zuquim, Hanna Tuomisto, Tomas Hrbek, Hiromitsu Sato & Camila Ribas
Several factors have been proposed as drivers of species diversification in the Neotropics, including environmental heterogeneity, the development of drainage systems and historical changes in forest distribution due to climatic oscillations. Here, we investigate which drivers contributed to the evolutionary history and current patterns of diversity of a polymorphic songbird (Arremon taciturnus) that is widely distributed in Amazonian and Atlantic forests as well as in Cerrado gallery and seasonally-dry forests. We use genomic, phenotypic and...

Maps of northern peatland extent, depth, carbon storage and nitrogen storage

Gustaf Hugelius, Julie Loisel, Sarah Chadburn, Robert B. Jackson, Miriam Jones, Glen MacDonald, Maija Marushchak, David Olefeldt, Maara Packalen, Matthias B. Siewert, Claire Treat, Merritt Turestsky, Carolina Voigt & Zicheng Yu
This dataset is grids of peatland extent, peat depth, peatland organic carbon storage, peatland total nitrogen storage and approximate extent of ombrotrophic/minerotrophic peatlands. The grids are geotiff files in 10 km pixel resolution projected in the World Azimuthal Equidistant projection. Note that the peat depth grid shows potential peat depth everywhere,also where there is no peatland cover. For files on peatland organic carbon, total nitrogen extent and extent of ombrotrophic/minerotrophic peatlands, there are separate files...

Robustness of the Dorsal morphogen gradient with respect to morphogen dosage

Gregory Reeves, Hadel Al Asafen, Sophia Carrell-Noel, Allison Schloop, Jeramey Friedman & Prasad Bandodkar
In multicellular organisms, the timing and placement of gene expression in a developing tissue assigns the fate of each cell in the embryo in order for a uniform field of cells to differentiate into a reproducible pattern of organs and tissues. This positional information is often achieved through the action of spatial gradients of morphogens. Spatial patterns of gene expression are paradoxically robust to variations in morphogen dosage, given that, by definition, gene expression must...

Exploring whole-genome duplicate gene retention with complex genetic interaction analysis

Elena Kuzmin, Benjamin VanderSluis, Alex N. Nguyen Ba, Wen Wang, Elizabeth N. Koch, Matej Usaj, Anton Khmelinskii, Mojca Mattiazzi Usaj, Jolanda Van Leeuwen, Oren Kraus, Amy Tresenrider, Michael Pryszlak, Ming-Che Hu, Brenda Varriano, Michael Costanzo, Michael Knop, Alan Moses, Chad L. Myers, Brenda J. Andrews & Charles Boone
Whole-genome duplication has played a central role in genome evolution of many organisms, including the human genome. Most duplicated genes are eliminated and factors that influence the retention of persisting duplicates remain poorly understood. Here, we describe a systematic complex genetic interaction analysis with yeast paralogs derived from the whole-genome duplication event. Mapping digenic interactions for a deletion mutant of each paralog and trigenic interactions for the double mutant provides insight into their roles and...

Data from: Plasticity and habitat choice match color to function in an ambush bug

Julia Boyle & Denon Start
Individuals aim to maximize their fitness by matching their own phenotype to the optimum phenotype in their environment. Individuals can achieve matching through several mechanism including habitat choice and adaptive plasticity. A key trait of interest to biologists is color, with background matching reciprocally camouflaging predators and prey. However, the multiple mechanisms matching an individual’s color to their background, and its consequences for function (e.g. species interactions), are rarely explored simultaneously. Here we investigate color...

Morphology and osteohistology of a large-bodied caenagnathid (Theropoda: Oviraptorosauria) from the Hell Creek Formation (Montana): implications for size-based classifications and growth reconstruction in theropods

Thomas Cullen, D. Jade Simon, Elizabeth Benner & David Evans
Oviraptorosaurs, like many coelurosaurians, are frequently diagnosed using incomplete or fragmentary skeletal remains, with factors such as body size often used to assign material to a particular taxon or as a basis for describing new species. Here we describe a partial skeleton, ROM VP 65884, from the Hell Creek Formation (Montana), and through morphological and phylogenetic comparisons identify it as belonging to Caenagnathidae, and likely referable to Anzu wyliei. We perform multi-element osteohistological sampling of...

Data from: Sampling schemes and drift can bias admixture proportions inferred by STRUCTURE

Ken Toyama, Pierre-André Crochet & Raphaël Leblois
The interbreeding of individuals coming from genetically differentiated but incompletely isolated populations can lead to the formation of admixed populations, having important implications in ecology and evolution. In this simulation study, we evaluate how individual admixture proportions estimated by the software structure are quantitatively affected by different factors. Using various scenarios of admixture between two diverging populations, we found that unbalanced sampling from parental populations may seriously bias the inferred admixture proportions; moreover, proportionally large...

Data from: Predators can influence the host-parasite dynamics of their prey via non-consumptive effects

Nicolette Zukowski, Devin Kirk, Kiran Wadhawan, Dylan Shea, Denon Start & Martin Krkosek
Ecological communities are partly structured by indirect interactions, where one species can indirectly affect another by altering its interactions with a third species. In the absence of direct predation, non-consumptive effects of predators on prey have important implications for subsequent community interactions. To better understand these interactions, we used a Daphnia-parasite-predator cue system to evaluate if predation risk affects Daphnia responses to a parasite. We investigated the effects of predator cues on two aspects of...

Data from: Oecanthus nigricornis (Orthoptera: Gryllidae) as the first known host of Stylogaster neglecta (Diptera: Conopidae)

Erik Etzler, William D. Brown, Luc F. Bussière & Darryl T. Gwynne
The conopid fly Stylogaster neglecta Williston (Diptera: Conopidae) is a parasitoid with no known host. We report this species as the first recorded dipteran parasitoid of Oecanthus nigricornis Walker (Orthoptera: Gryllidae) (black-horned tree crickets). We reared field-collected O. nigricornis juveniles over several months in 2017 and found that larval S. neglecta emerged from them during late July into August. We estimated the incubation period for S. neglecta larvae to be around 30 days based on...

S. neglecta parasitism in O. nigricornis: 2018 collection

Erik Etzler
In July 2018, we collected O. nigricornis crickets in southern Ontario (Canada) and New York State (United States of America): from the Koffler Scientific Reserve (coded as K or site 2) (King City Ontario, 44.03°N, 79.53°W), rare Charitable Research Reserve (coded as R or site 4) (Cambridge Ontario, 43.38°N, 80.39°W), the University of Toronto at Mississauga (coded as M or site 3) (43.55°N, 79.66°W), and the Edmund Niles Huyck Preserve and Biological Research Station (coded...

Recovery after the Rupture

Aarzoo Singh
The notion of home and belonging, specifically in the context of South Asian postcolonial diasporas, is connected to past traumas of colonization and displacement. This paper addresses how trauma, displacement, and colonialism can be understood through and with material culture, and how familial objects and items emit and/ or carry within them, emotional narratives. I turn to the affective currency that emit and are transferred on and down from objects, by diasporic subjects, to access...

Where New Words Are Born: Distributional Semantic Analysis of Neologisms and Their Semantic Neighborhoods

Maria Ryskina, Ella Rabinovich, Taylor Berg-Kirkpatrick, David R. Mortensen & Yulia Tsvetkov

WiDS (Women in Data Science) Datathon 2020: ICU Mortality Prediction

Meredith Lee, Jesse Raffa, Marzyeh Ghassemi, Tom Pollard, Sharada Kalanidhi, Omar Badawi, Karen Matthys & Leo Anthony Celi
WiDS (Women in Data Science) Datathon 2020: ICU Mortality Prediction focuses on patient health through data from MIT’s GOSSIS (Global Open Source Severity of Illness Score) initiative. Brought to you by the Global WiDS team, the West Big Data Innovation Hub, and the WiDS Datathon Committee, this year’s datathon is launching on Kaggle: bit.ly/WiDSdatathon2020kaggle.

Systematic genetics and single-cell imaging reveal widespread morphological pleiotropy and cell-to-cell variability.

Brenda Andrews
Our ability to understand the genotype-to-phenotype relationship is hindered by the lack of detailed understanding of phenotypes at a single-cell level. To systematically assess cell-to-cell phenotypic variability, we combined automated yeast genetics, high-content screening and neural network-based image analysis of single cells, focussing on genes that influence the architecture of four subcellular compartments of the endocytic pathway as a model system. Our unbiased assessment of the morphology of these compartments — endocytic patch, actin patch,...

A cross-sectional study of nemaline myopathy supplementary figures

Kimberly Amburgey, Meryl Acker, Samia Saeed, Reshma Amin, Alan H. Beggs, Carsten G. Bönneman, Michael Brudno, Andrei Constantinescu, Johannaz Dastgir, Mamadou Diallo, Casie A. Genetti, Michael Glueck, Stacy Hewson, Courtney Hum, Minal S. Jain, Michael W. Lawlor, Oscar H. Mayer, Leslie Nelson, Nicole Sultanum, Faiza Syed, Tuyen Tran, Ching H. Wang & James J. Dowling
Objective: Nemaline myopathy (NM) is a rare neuromuscular condition with clinical and genetic heterogeneity. To establish disease natural history, we performed a cross-sectional study of NM, complemented by longitudinal assessment and exploration of pilot outcome measures. Methods: Fifty-seven individuals with NM were recruited at two family workshops, including 16 examined at both time points. Subjects were evaluated by clinical history and physical examination. Functional outcome measures included the Motor Function Measure (MFM), pulmonary function tests...

Modelling the impact of antibody-dependent enhancement on disease severity of ZIKV and DENV sequential and co-infection

Biao Tang, Yanni Xiao, Beate Sander, Manisha A. Kulkarni & Jianhong Wu
Human infections with viruses of the genus Flavivirus, including dengue virus (DENV) and Zika virus (ZIKV), are of increasing global importance. Due to antibody dependent enhancement, secondary infection with one Flavivirus following primary infection with another {\it Flavivirus} can result in a significantly larger peak viral load with a much higher risk of severe disease. Although several mathematical models have been developed to quantify the virus dynamics in the primary and secondary infections of DENV,...

Behavioral, morphological, and ecological trait evolution in two clades of New World sparrows (Aimophila and Peucaea, Passerellidae)

Carla Cicero, Nicholas Mason, Lauryn Benedict & James Rising
The New World sparrows (Passerellidae) are a large and diverse group of songbirds that have been the subject of many studies on ecology, behavior, and evolutionary relationships. Here, we studied two clades of sparrows (Aimophila, Peucaea) to examine the evolution of behavioral, morphological, and ecological traits in a phylogenetic framework. Specifically, we inferred phylogenetic relationships in these clades, conducted ancestral state reconstructions, and asked whether patterns of trait evolution extend more broadly to New World...

Influence of local density and sex ratio on pollination in an ambophilous flowering plant

David Timerman & Spencer Barrett
PREMISE OF THE STUDY: Variation in local density and sex ratio in dioecious plants can affect mating success through the actions of pollen vectors, principally generalist insects or wind. Increased density and male-biased sex ratios should promote pollen transfer and seed production, but their combined effects have not been investigated for ambophilous species, which exhibit both insect and wind pollination. METHODS: We manipulated density (low vs. high) and sex ratio (1:1 vs. 3:1 male-biased) in...

A combined approach of mitochondrial DNA and anchored nuclear phylogenomics sheds light on unrecognized diversity, phylogeny, and historical biogeography of the cascade frogs, genus Amolops (Anura: Ranidae)

Yunhe Wu, Fang Yan, Bryan L. Stuart, Elizabeth Prendini, Chatmongkon Suwannapoom, Hollis A. Dahn, Bao-Lin Zhang, Hong-Xia Cai, Yong-Biao Xu, Ke Jiang, Hong-Man Chen, Alan R. Lemmon, Emily Moriarty Lemmon, Christopher J. Raxworthy, Nikolai L. Orlov, Robert W. Murphy & Jing Che
Amolops is one of the most species-rich genera in Ranidae, with 59 recognized species. This genus currently includes six species groups diagnosed mainly by morphology. Several recent molecular studies indicated that the classification of species groups within Amolops remains controversial, and key nodes in the phylogeny have been inadequately resolved. In addition, the diversity of cascade frogs remains poorly understood, especially for those from incompletely sampled regions. Herein, we investigate the species-level diversity within genus...

Phylogenetic signal and evolutionary correlates of urban tolerance in a widespread neotropical lizard clade

Kristin Winchell, Klaus P. Schliep, D. Luke Mahler & Liam J. Revell
Urbanization is intensifying worldwide, and while some species tolerate and even exploit urban environments, many others are excluded entirely from this new habitat. Understanding the factors that underlie tolerance of urbanization is thus of rapidly growing importance. Here we examine urban tolerance across a diverse group of lizards: Caribbean members of the neotropical genus Anolis. Our analyses reveal that urban tolerance has strong phylogenetic signal, suggesting that closely related species tend to respond similarly to...

Data from: Kin recognition in guppies uses self-referencing on olfactory cues

Mitchel Daniel & F. Helen Rodd
Kin recognition plays an important role in social behavior and evolution, but the proximate mechanisms by which individuals recognize kin remain poorly understood. In many species, individuals form a “kin template” that they compare against conspecifics’ phenotypes to assess phenotypic similarity–and by association, relatedness. Individuals may form a kin template through self-inspection (i.e. self-referencing) and/or by observing their rearing associates (i.e. family-referencing). However, despite much interest, few empirical studies have successfully disentangled self- and family-referencing....

Registration Year

  • 2020

Resource Types

  • Dataset
  • Text
  • Image


  • University of Toronto
  • Stanford University
  • McGill University
  • University of British Columbia
  • University of California, Berkeley
  • University of Alberta
  • University of Queensland
  • Royal Ontario Museum
  • University of Minnesota
  • University of Warwick