73 Works

Data from: Habitat preference facilitates successful early breeding in an open-cup nesting songbird

Ryan R. Germain, Richard Schuster, Kira E. Delmore & Peter Arcese
Selecting breeding habitats that ameliorate environmental limits on fitness and facilitate successful reproduction should benefit individual animals. This is particularly true in the temperate zone, where breeding early in a season presents a unique series of environmental challenges that can limit an individual's fitness. While many studies document links between habitat quality and reproductive success, few identify the cues used to assess habitat quality or the components of reproduction most influenced by occupying higher quality...

Data from: Prediction accuracies for growth and wood attributes of interior spruce in space using genotyping-by-sequencing

Omnia Gamal El-Dien, Blaise Ratcliffe, Jaroslav Klápste, Charles Chen, Ilga Porth & Yousry A. El-Kassaby
Background: Genomic selection (GS) in forestry can substantially reduce the length of breeding cycle and increase gain per unit time through early selection and greater selection intensity, particularly for traits of low heritability and late expression. Affordable next-generation sequencing technologies made it possible to genotype large numbers of trees at a reasonable cost. Results: Genotyping-by-sequencing was used to genotype 1,126 Interior spruce trees representing 25 open-pollinated families planted over three sites in British Columbia, Canada....

Data from: Double decomposition: decomposing the variance in subcomponents of male extra-pair reproductive success

Sylvain Losdat, Peter Arcese & Jane M. Reid
1. Extra-pair reproductive success (EPRS) is a key component of male fitness in socially monogamous systems and could cause selection on female extra-pair reproduction if extra-pair offspring (EPO) inherit high value for EPRS from their successful extra-pair fathers. However, EPRS is itself a composite trait that can be fully decomposed into subcomponents of variation, each of which can be further decomposed into genetic and environmental variances. However, such decompositions have not been implemented in wild...

Data from: Evaluating methods for estimating local effective population size with and without migration

Kimberly Julie Gilbert & Michael C. Whitlock
Effective population size is a fundamental parameter in population genetics, evolutionary biology and conservation biology, yet its estimation can be fraught with difficulties. Several methods to estimate Ne from genetic data have been developed which take advantage of various approaches for inferring Ne. The ability of these methods to accurately estimate Ne, however, has not been comprehensively examined. In this study, we employ seven of the most cited methods for estimating Ne from genetic data...

Data from: A comparison of genomic selection models across time in interior spruce (Picea engelmannii × glauca) using unordered SNP imputation methods

Blaise Ratcliffe, Omnia Gamal El-Dien, Jaroslav Klápště, Ilga Porth, Charles Chen, Barry Jaquish & Yousry A. El-Kassaby
Genomic selection (GS) potentially offers an unparalleled advantage over traditional pedigree-based selection (TS) methods by reducing the time commitment required to carry out a single cycle of tree improvement. This quality is particularly appealing to tree breeders, where lengthy improvement cycles are the norm. We explored the prospect of implementing GS for interior spruce (Picea engelmannii × glauca) utilizing a genotyped population of 769 trees belonging to 25 open-pollinated families. A series of repeated tree...

Data from: Acceleration and novelty: community restoration speeds recovery and transforms species composition in Andean cloud forest

Sarah Jane Wilson & Jeanine M. Rhemtulla
Community-based tropical forest restoration projects, often promoted as a win-win solution for local communities and the environment, have increased dramatically in number in the past decade. Many such projects are underway in Andean cloud forests, which, given their extremely high biodiversity and history of extensive clearing, are understudied. This study investigates the efficacy of community-based tree-planting projects to accelerate cloud forest recovery, as compared to unassisted natural regeneration. This study takes place in northwest Andean...

Data from: The origin and evolution of phototropins

Fay-Wei Li, Kathleen M. Pryer, Gane K.-S. Wong, Carl J. Rothfels, Michael Melkonian, Sarah Mathews, Juan C. Villarreal & Sean W. Graham
Plant phototropism, the ability to bend toward or away from light, is predominantly controlled by blue-light photoreceptors, the phototropins. Although phototropins have been well-characterized in Arabidopsis thaliana, their evolutionary history is largely unknown. In this study, we complete an in-depth survey of phototropin homologs across land plants and algae using newly available transcriptomic and genomic data. We show that phototropins originated in an ancestor of Viridiplantae (land plants + green algae). Phototropins repeatedly underwent independent...

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: Previously unknown evolutionary groups dominate the ssDNA gokushoviruses in oxic and anoxic waters of a coastal marine environment

Jessica M. Labonté, Steven J. Hallam & Curtis A. Suttle
Metagenomic studies have revealed that ssDNA phages from the family Microviridae subfamily Gokushovirinae are widespread in aquatic ecosystems. It is hypothesized that gokushoviruses occupy specialized niches, resulting in differences among genotypes traversing water column gradients. Here, we use degenerate primers that amplify a fragment of the gene encoding the major capsid protein to examine the diversity of gokushoviruses in Saanich Inlet, a seasonally anoxic fjord on the coast of Vancouver Island, British Columbia. Amplicon sequencing...

Data from: The relative power of genome scans to detect local adaptation depends on sampling design and statistical method

Katie E. Lotterhos & Michael C. Whitlock
Although genome scans have become a popular approach towards understanding the genetic basis of local adaptation, the field still does not have a firm grasp on how sampling design and demographic history affect the performance of genome scans on complex landscapes. To explore these issues, we compared 20 different sampling designs in equilibrium (i.e. island model and isolation by distance) and nonequilibrium (i.e. range expansion from one or two refugia) demographic histories in spatially heterogeneous...

Data from: Genetic architecture and genomic patterns of gene flow between hybridizing species of Picea

Amanda De La Torre, Pär Ingvarsson & Sally N. Aitken
Hybrid zones provide an opportunity to study the effects of selection and gene flow in natural settings. We employed nuclear microsatellites (single sequence repeat (SSR)) and candidate gene single-nucleotide polymorphism markers (SNPs) to characterize the genetic architecture and patterns of interspecific gene flow in the Picea glauca × P. engelmannii hybrid zone across a broad latitudinal (40–60 degrees) and elevational (350–3500 m) range in western North America. Our results revealed a wide and complex hybrid...

Data from: Genetic relationships between Atlantic and Pacific populations of the notothenioid fish Eleginops maclovinus: the footprints of Quaternary glaciations in Patagonia

Santiago G. Ceballos, Enrique P. Lessa, Roberto Licandeo & Daniel A. Fernandez
The genetic relationships between the Pacific and the Atlantic populations of marine costal biota in Southern South America have been analyzed in few studies, most of them relying on a single mitochondrial locus. We analyzed ten polymorphic microsatellite loci, isolated from a dinucleotide-enriched E. maclovinus genomic library, in a total of 240 individuals (48 from each of five sampled sites: two Atlantic, two Pacific and one in Beagle Channel). The results were contrasted against a...

Data from: Intraguild predation leads to genetically based character shifts in the threespine stickleback

Sara E. Miller, Daniel Metcalf & Dolph Schluter
Intraguild predation is a common ecological interaction that occurs when a species preys upon another species with which it competes. The interaction is potentially a mechanism of divergence between intraguild prey populations, but it is unknown if cases of character shifts in intraguild prey are an environmental or evolutionary response. We investigated the genetic basis and inducibility of character shifts in threespine stickleback from lakes with and without prickly sculpin, a benthic intraguild predator. Wild...

Data from: Effects of climate change on habitat availability and configuration for an endemic coastal alpine bird

Michelle M. Jackson, Sarah E. Gergel & Kathy Martin
North America’s coastal mountains are particularly vulnerable to climate change, yet harbour a number of endemic species. With little room “at the top” to track shifting climate envelopes, alpine species may be especially negatively affected by climate-induced habitat fragmentation. We ask how climate change will affect the total amount, mean patch size, and number of patches of suitable habitat for Vancouver Island White-tailed Ptarmigan (Lagopus leucura saxatilis; VIWTP), a threatened, endemic alpine bird. Using a...

Data from: Responses to simulated winter conditions differ between threespine stickleback ecotypes

Taylor C. Gibbons, Seth M. Rudman & Patricia M. Schulte
Abiotic factors can act as barriers to colonization and drive local adaptation. During colonization, organisms may cope with changes in abiotic factors using existing phenotypic plasticity, but the role of phenotypic plasticity in assisting or hindering the process of local adaptation remains unclear. To address these questions, we explore the role of winter conditions in driving divergence during freshwater colonization and the effects of plasticity on local adaptation in ancestral marine and derived freshwater ecotypes...

Data from: Predators modify the evolutionary response of prey to temperature change

Michelle Tseng & Mary I. O'Connor
As climate regimes shift in many ecosystems worldwide, evolution may be a critical process allowing persistence in rapidly changing environments. Organisms regularly interact with other species, yet whether climate-mediated evolution can occur in the context of species interactions is not well understood. We tested whether a species interaction could modify evolutionary responses to temperature. We demonstrate that predation pressure by Dipteran larvae (Chaoborus americanus) modified the evolutionary response of a freshwater crustacean (Daphnia pulex) to...

Data from: Nutrient foraging behaviour of four co-occuring perennial grassland plant species alone does not predict behaviour with neighbours

Gordon G. McNickle, Michael K. Deyholos, & James F. Cahill
The spatial arrangement of nutrients and neighbours in soil influences plant growth and reproduction. Plants often respond to such stimuli through plasticity in root proliferation (root mass per soil volume), or the breadth of their root system. Here, we asked how plants adjust nutrient foraging strategies when grown alone or with neighbours. We asked (i) Does root proliferation into nutrient-rich patches when plants are grown alone predict root proliferation when plants are grown with neighbours?...

Data from: Morphological and genetic analysis of sympatric dace within the Rhinichthys cataractae species complex: a case of isolation lost

Jennifer A. Ruskey & Eric B. Taylor
The Nooksack dace (Pisces: an undescribed putative taxon within Rhinichthys) and longnose dace (Rhinichthys cataractae) are two forms within the R. cataractae species complex that are distinguishable from one another by mitochondrial (mt) DNA divergence of 2–3%, as well as by subtle morphological differences. The two forms are found in allopatry in south-eastern British Columbia (BC), Canada, and adjacent areas of western Washington, USA, and are sympatric in three streams in the lower Fraser River...

Data from: Resolving the conundrum of inbreeding depression but no inbreeding avoidance: estimating sex-specific selection on inbreeding by song sparrows (Melospiza melodia)

Jane M. Reid, Peter Arcese, Greta Bocedi, Alexander Bradley Duthie, Matthew Ernest Wolak & Lukas F. Keller
Inbreeding avoidance among interacting females and males is not always observed despite inbreeding depression in offspring fitness, creating an apparent ‘inbreeding paradox’. This paradox could be resolved if selection against inbreeding was in fact weak, despite inbreeding depression. However, the net magnitude and direction of selection on the degree to which females and males inbreed by pairing with relatives has not been explicitly estimated. We used long-term pedigree data to estimate phenotypic selection gradients on...

Data from: Life-history characteristics and landscape attributes as drivers of genetic variation, gene flow and fine-scale population structure in Northern Dolly Varden (Salvelinus malma malma) in Canada

Les N. Harris, Robert Bajno, Colin P. Gallagher, Itsuro Koizumi, Lucy K. Johnson, Kimberly L. Howland, Eric B. Taylor & James D. Reist
The Northern Dolly Varden (Salvelinus malma malma) displays variable life-history types and occupies freshwater habitats with varying levels of connectivity. Here, we assayed microsatellite DNA variation in Northern Dolly Varden from the western Canadian Arctic to resolve landscape and life history variables driving variation in genetic diversity and population structure. Overall, genetic variation was highest in anadromous populations and lowest in those isolated above waterfalls with stream-resident forms intermediate between the two. Anadromous and isolated...

Data from: The new Andean jumping spider genus Urupuyu and its placement within a revised classification of the Amycoida (Araneae: Salticidae)

Gustavo R.S. Ruiz & Wayne P. Maddison
Urupuyu gen. nov. is described for three new species of small black jumping spiders from the cloud forests of Ecuador: Urupuyu antisana sp. nov. (type species), U. edwardsi sp. nov., and U. occidentale sp. nov. Phylogenetic analyses with DNA sequences (28S, actin 5C, wingless, 16SND1 and CO1) indicate Urupuyu is closely related to the huriine amycoids Hurius and Scoturius, a placement also supported by morphological traits. Our phylogenetic analysis serves to clarify the relationships within...

Data from: Phylogenomics and historical biogeography of the monocot order Liliales: out of Australia and through Antarctica

Thomas J. Givnish, Alejandro Zuluaga, Isabel Marques, Vivienne K. Y. Lam, Marybel Soto Gomez, William J. D. Iles, Mercedes Ames, Daniel Spalink, Jackson R. Moeller, Barbara G. Briggs, Stephanie P. Lyon, Dennis W. Stevenson, Wendy Zomlefer & Sean W. Graham
We present the first phylogenomic analysis of relationships among all ten families of Liliales, based on 75 plastid genes from 35 species in 29 genera, and 97 additional plastomes stratified across angiosperm lineages. We used a supermatrix approach to extend our analysis to 58 of 64 genera of Liliales, and calibrated the resulting phylogeny against 17 fossil dates to produce a new timeline for monocot evolution. Liliales diverged from other monocots 124 Mya and began...

Data from: Warming alters food web-driven changes in the CO2 flux of experimental pond ecosystems

Trisha B. Atwood, Edd Hammill, Pavel Kratina, Hamish S. Greig, Jonathan B. Shurin & John S. Richardson
Evidence shows the important role biota play in the carbon cycle, and strategic management of plant and animal populations could enhance CO2 uptake in aquatic ecosystems. However, it is currently unknown how management-driven changes to community structure may interact with climate warming and other anthropogenic perturbations to alter CO2 fluxes. Here we showed that under ambient water temperatures, predators (three-spined stickleback) and nutrient enrichment synergistically increased primary producer biomass, resulting in increased CO2 uptake by...

Data from: Patterns and drivers of intraspecific variation in avian life history along elevational gradients: a meta-analysis

W. Alice Boyle, Brett K. Sandercock & Kathy Martin
Elevational gradients provide powerful natural systems for testing hypotheses regarding the role of environmental variation in the evolution of life-history strategies. Case studies have revealed shifts towards slower life histories in organisms living at high elevations yet no synthetic analyses exist of elevational variation in life-history traits for major vertebrate clades. We examined (i) how life-history traits change with elevation in paired populations of bird species worldwide, and (ii) which biotic and abiotic factors drive...

Data from: Whole plastome sequencing reveals deep plastid divergence and cytonuclear discordance between closely related balsam poplars, Populus balsamifera and P. trichocarpa (Salicaceae)

Daisie I. Huang, Charles A. Hefer, Natalia Kolosova, Carl J. Douglas & Quentin C. B. Cronk
As molecular phylogenetic analyses incorporate ever-greater numbers of loci, cases of cytonuclear discordance – the phenomenon in which nuclear gene trees deviate significantly from organellar gene trees – are being reported more frequently. Plant examples of topological discordance, caused by recent hybridization between extant species, are well known. However, examples of branch-length discordance are less reported in plants relative to animals. We use a combination of de novo assembly and reference-based mapping using short-read shotgun...

Registration Year

  • 2015
    73

Resource Types

  • Dataset
    73

Affiliations

  • University of British Columbia
    73
  • University of Alberta
    6
  • Duke University
    3
  • University of Aberdeen
    3
  • University of California, Berkeley
    3
  • The Bronx Defenders
    2
  • Centre for Australian National Biodiversity Research
    2
  • University of Cologne
    2
  • Oregon State University
    2
  • University of Minnesota
    2