180 Works

Data from: Chemical element distributions within conodont elements and their functional implications

Erik Cowing Katvala & Charles M. Henderson
Electron microprobe analyses of platform (pectiniform Pa) elements of Permian conodonts reveal detailed and systematic chemical element distributions. The crown of the conodont element is more densely mineralized than the basal body and shows evidence of less dense mineralization in areas of rapid growth. Patterns in sodium and sulfur concentrations indicate oral to aboral differentiation within conodont elements. These chemical element patterns support oral exposure during life and functional use as a tooth, and they...

Data from: Targeted capture and resequencing of 1040 genes reveal environmentally driven functional variation in gray wolves

Rena M. Schweizer, Jacqueline Robinson, Ryan Harrigan, Pedro Silva, Marco Galaverni, Marco Musiani, Richard E. Green, John Novembre & Robert K. Wayne
In an era of ever-increasing amounts of whole genome sequence data for individuals and populations, the utility of traditional single nucleotide polymorphisms (SNPs) array-based genome scans is uncertain. We previously performed a SNP array-based genome scan to identify candidate genes under selection in six distinct gray wolf (Canis lupus) ecotypes. Using this information, we designed a targeted capture array for 1040 genes, including all exons and flanking regions, as well as 5000 1 kb non-genic...

Data from: Phylogeography of the prickly sculpin (Cottus asper) in north-western North America reveals parallel phenotypic evolution across multiple coastal–inland colonizations

Stefan Dennenmoser, Arne W. Nolte, Steven M. Vamosi & Sean M. Rogers
Aim: Glacial cycles during the Pleistocene may have frequently contributed to parallel evolution of phenotypes across independently evolving genetic lineages associated with separate glacial refugia. Previous studies based on morphology suggested that the prickly sculpin (Cottus asper) survived the Last Glacial Maximum (LGM) in southern coastal and inland refugia, favouring allopatric divergence between coastal and inland prickling phenotypes, which vary in the degree to which spine-like scales cover the body of the fish. Herein, we...

Data from: Successful carnivore identification with faecal DNA across a fragmented Amazonian landscape

Fernanda Michalski, Fernanda Pedone Valdez, Darren Norris, Chris Zieminski, Cyntia Kayo Kashivakura, Cristine S. Trinca, Heath B. Smith, Carly Vynne, Samuel K. Wasser, Jean Paul Metzger & Eduardo Eizirik
The use of scat surveys to obtain DNA has been well documented in temperate areas, where DNA preservation may be more effective than in tropical forests. Samples obtained in the tropics are often exposed to high humidity, warm temperatures, frequent rain, and intense sunlight, all of which can rapidly degrade DNA. Despite these potential problems, we demonstrate successful DNA amplification and sequencing for faeces of carnivores collected in tropical conditions and quantify how sample condition...

Data from: Population extinctions can increase metapopulation persistence

Jeremy W. Fox, David Vasseur, Morgan Cotroneo, Lilian Guan & Franz Simon
Metapopulations persist when local populations are rapidly recolonized following local extinctions. Such persistence requires asynchrony; simultaneous crashes of all populations would leave no source of recolonization. We show theoretically and experimentally that catastrophic population extinctions themselves can promote metapopulation persistence, by preventing spatial synchrony and thus enhancing recolonization. We refer to this behaviour as the ‘spatial hydra effect’: as with the mythical hydra that grows two new heads when one is removed, extinctions can increase...

Data from: Closely coupled evolutionary history of ecto- and endosymbionts from two distantly related animal phyla

Judith Zimmermann, Cecilia Wentrup, Miriam Sadowski, Anna Blazejak, Harald R. Gruber-Vodicka, Manuel Kleiner, Joerg A. Ott, Bodil Cronholm, Pierre De Wit, Christer Erséus & Nicole Dubilier
The level of integration between associated partners can range from ectosymbioses to extracellular and intracellular endosymbioses, and this range has been assumed to reflect a continuum from less intimate to evolutionarily highly stable associations. In this study, we examined the specificity and evolutionary history of marine symbioses in a group of closely related sulphur-oxidizing bacteria, called Candidatus Thiosymbion, that have established ecto- and endosymbioses with two distantly related animal phyla, Nematoda and Annelida. Intriguingly, in...

Data from: Quantifying how constraints limit the diversity of viable routes to adaptation

Samuel Yeaman, Aleeza C. Gerstein, Kathryn A. Hodgins, Michael C. Whitlock & Sam Yeaman
Convergent adaptation can occur at the genome scale when independently evolving lineages use the same genes to respond to similar selection pressures. These patterns provide insights into the factors that facilitate or constrain the diversity of genetic responses that contribute to adaptive evolution. A first step in studying such factors is to quantify the observed amount of repeatability relative to expectations under a null hypothesis. Here, we formulate a novel metric to quantify the constraints...

Data from: NEMBASE4: the nematode transcriptome resource

Mark L. Blaxter, James Wasmuth, Benjamin Elsworth & Mark Blaxter
Nematode parasites are of major importance in human health and agriculture, and free-living species deliver essential ecosystem services. The genomics revolution has resulted in the production of many datasets of expressed sequence tags (ESTs) from a phylogenetically wide range of nematode species, but these are not easily compared. NEMBASE4 presents a single portal onto extensively functionally annotated, EST-derived transcriptomes from over sixty species of nematodes, including plant and animal parasites and free-living taxa. Using the...

Data from: Occasional long-distance dispersal increases spatial synchrony of population cycles

Jessica Hopson & Jeremy W. Fox
1. Spatially-separated populations of the same species often exhibit correlated fluctuations in abundance, a phenomenon known as spatial synchrony. Dispersal can generate spatial synchrony. In nature, most individuals disperse short distances with a minority dispersing long distances. The effect of occasional long-distance dispersal on synchrony is untested, and theoretical predictions are contradictory. Occasional long-distance dispersal might either increase both overall synchrony and the spatial scale of synchrony, or reduce them. 2. We conducted a protist...

Data from: Primates adjust movement strategies due to changing food availability

Rafael Reyna-Hurtado, Julie A. Teichroeb, Tyler R. Bonnell, Raul Uriel Hernández-Sarabia, Sofia M. Vickers, Juan Carlos Serio-Silva, Pascale Sicotte & Colin A. Chapman
Animals are hypothesized to search their environments in predictable ways depending on the distribution of resources. Evenly distributed foods are thought to be best exploited with random Brownian movements; while foods that are patchy or unevenly distributed require non-Brownian strategies, such as Lévy walks. Thus, when food distribution changes due to seasonal variation, animals should show concomitant changes in their search strategies. We examined this issue in six monkey species from Africa and Mexico: three...

Data from: Dioecy does not consistently accelerate or slow lineage diversification across multiple genera of angiosperms

Niv Sabath, Emma E. Goldberg, Lior Glick, Moshe Einhorn, Tia-Lynn Ashman, Ray Ming, Sarah P. Otto, Jana Vamosi, Itay Mayrose & Jana C. Vamosi
Dioecy, the sexual system in which male and female organs are found in separate individuals, allows greater specialization for sex-specific functions and can be advantageous under various ecological and environmental conditions. However, dioecy is rare among flowering plants. Previous studies identified contradictory trends regarding the relative diversification rates of dioecious lineages vs their nondioecious counterparts, depending on the methods and data used. We gathered detailed species-level data for dozens of genera that contain both dioecious...

Data from: Trophic interactions and abiotic factors drive functional and phylogenetic structure of vertebrate herbivore communities across the Arctic tundra biome

James D.M. Speed, Ina A. Skjelbred, Isabel C. Barrio, Michael D. Martin, Dominique Berteaux, C. Guillermo Bueno, Katie S. Christie, Bruce C. Forbes, Jennifer Forbey, Daniel Fortin, Jon-Arvid Grytnes, Katrine S. Hoset, Nicolas Lecomte, Bryndis Marteinsdottir, Jesper B. Mosbacher, Åshild O. Pedersen, Virve Ravolainen, Eileen C. Rees, Anna Skarin, Natalya Sokolova, Andrew H. Thornhill, Ingunn Tombre & Eeva M. Soininen
Communities are assembled from species that evolve or colonise a given geographic region, and persist in the face of abiotic conditions and interactions with other species. The evolutionary and colonisation histories of communities are characterised by phylogenetic diversity, while functional diversity is indicative of abiotic and biotic conditions. The relationship between functional and phylogenetic diversity infers whether species functional traits are divergent (differing between related species) or convergent (similar among distantly related species). Biotic interactions...

Data from: The extended Price equation quantifies species selection on mammalian body size across the Palaeocene/Eocene Thermal Maximum

Brian D. Rankin, Jeremy W. Fox, Christian R. Barrón-Ortiz, Amy E. Chew, Patricia A. Holroyd, Joshua A. Ludtke, Xingkai Yang & Jessica M. Theodor
Species selection, covariation of species’ traits with their net diversification rates, is an important component of macroevolution. Most studies have relied on indirect evidence for its operation and have not quantified its strength relative to other macroevolutionary forces. We use an extension of the Price equation to quantify the mechanisms of body size macroevolution in mammals from the latest Palaeocene and earliest Eocene of the Bighorn and Clarks Fork Basins of Wyoming. Dwarfing of mammalian...

Data from: Variation in ligand responses of the bitter taste receptors TAS2R1 and TAS2R4 among New World monkeys

Kei Tsutsui, Masahiro Otoh, Kodama Sakurai, Nami Suzuki-Hashido, Takashi Hayakawa, Takumi Misaka, Yoshiro Ishimaru, Filippo Aureli, Amanda D. Melin, Shoji Kawamura & Hiroo Imai
Background: New World monkeys (NWMs) are unique in that they exhibit remarkable interspecific variation in color vision and feeding behavior, making them an excellent model for studying sensory ecology. However, it is largely unknown whether non-visual senses co-vary with feeding ecology, especially gustation, which is expected to be indispensable in food selection. Bitter taste, which is mediated by bitter taste receptors (TAS2Rs) in the tongue, helps organisms avoid ingesting potentially toxic substances in food. In...

Data from: Phylogenomic reconstruction of sportive lemurs (genus Lepilemur) recovered from mitogenomes with inferences for Madagascar biogeography

Runhua Lei, Cynthia L. Frasier, Melissa T.R. Hawkins, Shannon E. Engberg, Carolyn A. Bailey, Steig E. Johnson, Adam T. McLain, Colin P. Groves, George H. Perry, Stephen D. Nash, Russell A. Mittermeier &
The family Lepilemuridae includes 26 species of sportive lemurs, most of which were recently described. The cryptic morphological differences confounded taxonomy until recent molecular studies; however, some species’ boundaries remain uncertain. To better understand the genus Lepilemur, we analyzed 35 complete mitochondrial genomes representing all recognized 26 sportive lemur taxa and estimated divergence dates. With our dataset we recovered 25 reciprocally monophyletic lineages, as well as an admixed clade containing Lepilemur mittermeieri and Lepilemur dorsalis....

Data from: Genetic population structure in prickly sculpin (Cottus asper) reflects isolation by environment between two life history ecotypes

Stefan Dennenmoser, Sean M. Rogers & Steven M. Vamosi
Life-history transitions have evolved repeatedly in numerous taxa, although the ecological and evolutionary conditions favouring such transitions in the presence of gene flow remain poorly understood. The present study aimed to disentangle the effects of isolation-by-distance and isolation-by-environment on genetic differentiation between two sympatric life-history ecotypes. Using 14 microsatellite loci, we first characterized amphidromous and freshwater groups of Cottus asper in a high gene flow setting in the Lower Fraser River system (south-western British Columbia,...

Data from: Macroevolutionary synthesis of flowering plant sexual systems

Emma E. Goldberg, Sarah P. Otto, Jana C. Vamosi, Itay Mayrose, Niv Sabath, Ray Ming & Tia-Lynn Ashman
Sexual system is a key determinant of genetic variation and reproductive success, affecting evolution within populations and within clades. Much research in plants has focused on evolutionary transitions away from the most common state of hermaphroditism and toward the rare state of dioecy (separate sexes). Rather than transitions predominantly toward greater sexual differentiation, however, evolution may proceed in the direction of lesser sexual differentiation. We analyzed the macroevolutionary dynamics of sexual system in angiosperm genera...

Data from: Deletion/loss of bone morphogenetic protein 7 changes tooth morphology and function in Mus musculus: implications for dental evolution in mammals

Chelsey Zurowski, Heather Jamniczky, Daniel Graf & Jessica Theodor
Quantifying regulatory gene effects on dental morphology and function has implications for the underlying mechanisms that generated dental diversity in mammals. We tested the hypothesis that regulatory gene expression changes lead to differences in molars using a neural crest knockout of bone morphogenetic protein 7 (BMP7) in Mus musculus. 3D geometric morphometric methods were used to quantify the shape of the molar toothrow. BMP7 mutants have extra cusps on the first upper and lower molars,...

Data from: Female sociality and sexual conflict shape offspring survival in a Neotropical primate

Urs Kalbitzer, Mackenzie L. Bergstrom, Sarah D. Carnegie, Eva C. Wikberg, Shoji Kawamura, Fernando A. Campos, Katharine M. Jack & Linda M. Fedigan
Most mammals live in social groups in which members form differentiated social relationships. Individuals may vary in their degree of sociality, and this variation can be associated with differential fitness. In some species, for example, female sociality has a positive effect on infant survival. However, investigations of such cases are still rare, and no previous study has considered how male infanticide might constrain effects of female sociality on infant survival. Infanticide is part of the...

Data from: The consequences of demand-driven seed provisioning for sexual differences in reproductive investment in Thalictrum occidentale (Ranunculaceae)

Takashi Y. Ida, Lawrence D. Harder & Gaku Kudo
Many iteroparous angiosperms may benefit from flexible annual resource allocation in response to variable reproductive opportunities induced by external conditions. If maximal reproductive investment is fixed, lack of reproductive sinks would cause resource redistribution to other sinks. Alternatively, reproductive investment may vary depending on the demand of reproductive sinks, changing source-sink relations. In particular, differential responses by males and females to the demands of flower and seed production may cause sexual dimorphism. We assess the...

Data from: Transcriptome analysis of 20 taxonomically related benzylisoquinoline alkaloid-producing plants

Jillian M. Hagel, Jeremy S. Morris, Eun-Jeong Lee, Isabel Desgagné-Penix, Crystal D. Bross, Limei Chang, Xue Chen, Scott C. Farrow, Ye Zhang, Jung Soh, Christoph W. Sensen & Peter J. Facchini
Background: Benzylisoquinoline alkaloids (BIAs) represent a diverse class of plant specialized metabolites sharing a common biosynthetic origin beginning with tyrosine. Many BIAs have potent pharmacological activities, and plants accumulating them boast long histories of use in traditional medicine and cultural practices. The decades-long focus on a select number of plant species as model systems has allowed near or full elucidation of major BIA pathways, including those of morphine, sanguinarine and berberine. However, this focus has...

Data from: Shape-shift: semicircular canal morphology responds to selective breeding for increased locomotor activity

Heidi Schutz, Heather A. Jamniczky, Benedikt Hallgrímsson, & Theodore Garland
Variation in semicircular canal morphology correlates with locomotor agility among species of mammals. An experimental evolutionary mouse model was used to test the hypotheses that semicircular canal morphology (1) evolves in response to selective breeding for increased locomotor activity, (2) exhibits phenotypic plasticity in response to early-onset chronic exercise, and (3) is unique in individuals possessing the minimuscle phenotype. We examined responses in canal morphology to prolonged wheel access and selection in laboratory mice from...

Data from: Reproductive aging patterns in primates reveal that humans are distinct

Susan C. Alberts, Jeanne Altmann, Diane K. Brockman, Marina Cords, Linda M. Fedigan, Anne Pusey, Tara S. Stoinski, Karen B. Strier, William F. Morris & Anne M. Bronikowski
Women rarely give birth after approximately 45 years of age, and they experience the cessation of reproductive cycles – menopause – at approximately 50 years of age, after a fertility decline lasting almost two decades. Such reproductive senescence in mid-lifespan is an evolutionary puzzle of enduring interest because it should be inherently disadvantageous. Further, comparative data on reproductive senescence from other primates, or indeed other mammals, remains relatively rare. Here we carried out the first...

Data from: Contemporary ancestor? Adaptive divergence from standing genetic variation in Pacific marine threespine stickleback

Matthew Richard John Morris, Ella Bowles, Brandon Eugene Allen, Heather A. Jamniczky & Sean M. Rogers
Background: Populations that have repeatedly colonized novel environments are useful for studying the role of ecology in adaptive divergence - particularly if some individuals persist in the ancestral habitat. Such "contemporary ancestors" can be used to demonstrate the effects of selection by comparing phenotypic and genetic divergence between the derived population and their extant ancestors. However, evolution and demography in these "contemporary ancestors" can complicate inferences about the source (standing genetic variation, de novo mutation)...

Data from: Enamel hypoplasia and dental wear of North American late Pleistocene horses and bison: an assessment of nutritionally-based extinction models

Christina I. Barrón-Ortiz, Christopher N. Jass, Raúl Barrón-Corvera, Jennifer Austen & Jessica M. Theodor
Approximately 50,000 – 11,000 years ago many species around the world became extinct or were extirpated at a continental scale. The causes of the late Pleistocene extinctions have been extensively debated and continue to be poorly understood. Several extinction models have been proposed, including two nutritionally-based extinction models: coevolutionary disequilibrium and mosaic-nutrient models. These models draw upon the individualistic response of plant species to climate change to present a plausible scenario in which nutritional stress...

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