73 Works

Data from: Genomic analysis of a migratory divide reveals candidate genes for migration and implicates selective sweeps in generating islands of differentiation

Kira E. Delmore, Sariel Hübner, Nolan C. Kane, Richard Schuster, Rose L. Andrew, Francisco Câmara, Roderic Guigo & Darren E. Irwin
Differential gene flow, reductions in diversity following linked selection and/or features of the genome can structure patterns of genomic differentiation during the process of speciation. Possible sources of reproductive isolation are well studied between coastal and inland subspecies groups of Swainson's thrushes, with differences in seasonal migratory behaviour likely playing a key role in reducing hybrid fitness. We assembled and annotated a draft reference genome for this species and generated whole-genome shotgun sequence data for...

Data from: Recent Y chromosome divergence despite ancient origin of dioecy in poplars (Populus)

Armando Geraldes, Charles A. Hefer, Arnaud Capron, Natalia Kolosova, Felix Martinez-Nuñez, Raju Y. Soolanayakanahally, Brian Stanton, Robert D. Guy, Shawn D. Mansfield, Carl J. Douglas & Quentin C. B. Cronk
All species of the genus Populus (poplar, aspen) are dioecious, suggesting an ancient origin of this trait. Despite some empirical counter examples, theory suggests that nonrecombining sex-linked regions should quickly spread, eventually becoming heteromorphic chromosomes. In contrast, we show using whole-genome scans that the sex-associated region in Populus trichocarpa is small and much younger than the age of the genus. This indicates that sex determination is highly labile in poplar, consistent with recent evidence of...

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...

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: 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: 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: 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: 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: Genetic evidence for ecological divergence in kokanee salmon

Matthew A. Lemay & Michael A. Russello
The evolution of locally adapted phenotypes among populations that experience divergent selective pressures is a central mechanism for generating and maintaining biodiversity. Recently, the advent of high-throughput DNA sequencing technology has provided tools for investigating the genetic basis of this process in natural populations of non-model organisms. Kokanee, the freshwater form of sockeye salmon (Oncorhynchus nerka), occurs as two reproductive ecotypes, which differ in spawning habitat (tributaries vs. shorelines), however outside of the spawning season...

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: A simple approach for maximizing the overlap of phylogenetic and comparative data

Matthew W. Pennell, Richard G. FitzJohn & William K. Cornwell
Biologists are increasingly using curated, public data sets to conduct phylogenetic comparative analyses. Unfortunately, there is often a mismatch between species for which there is phylogenetic data and those for which other data are available. As a result, researchers are commonly forced to either drop species from analyses entirely or else impute the missing data. A simple strategy to improve the overlap of phylogenetic and comparative data is to swap species in the tree that...

Data from: The conservation value of high elevation habitats to North American migrant birds

W. Alice Boyle & Kathy Martin
The basic patterns of faunal community composition and habitat associations of high elevation mountainous regions are poorly-known. This is true for the avifauna of western North America where our knowledge of high elevation use is primarily restricted to breeding assemblages. Here we report on systematic avian surveys of high elevation habitats over four years in British Columbia conducted during the post-breeding and fall migration periods (Aug–Oct). We detected a remarkable diversity of birds (95 species...

Data from: Historical dynamics of ecosystem services bundles

Delphine Renard, Jeanine M. Rhemtulla & Elena M. Bennett
Managing multiple ecosystem services (ES), including addressing trade-offs between services and preventing ecological surprises, is among the most pressing areas for sustainability research. These challenges require ES research to go beyond the currently common approach of snapshot studies limited to one or two services at a single point in time. We used a spatiotemporal approach to examine changes in nine ES and their relationships from 1971 to 2006 across 131 municipalities in a mixed-use landscape...

Data from: Shared genetic diversity across the global invasive range of the Monk parakeet suggests a common restricted geographic origin and the possibility of convergent selection

Pim Edelaar, Severine Roques, Elizabeth A. Hobson, Anders Gonçalves Da Silva, Michael L. Avery, Michael A. Russello, Juan Carlos Senar, Timothy F. Wright, Martina Carrete & Jose Luis Tella
While genetic diversity is hypothesized to be an important factor explaining invasion success, there is no consensus yet on how variation in source populations or demographic processes affects invasiveness. We used mitochondrial DNA haplotypic and microsatellite genotypic data to investigate levels of genetic variation and reconstruct the history of replicate invasions on three continents in a globally invasive bird, the monk parakeet (Myiopsitta monachus). We evaluated whether genetic diversity at invasive sites could be explained...

Data from: Rethinking refugia: tree topology, divergence dates, and demographic history trace the distribution of the endangered Plymouth gentian (Sabatia kennedyana) from the Pleistocene glaciation to present day

Adriana Suarez-Gonzalez, Jolene T. Sutton, Andrew J. Trant, Elena Zamlynny & Sara V. Good
Premise of study: Molecular population genetics is a powerful tool to infer how species responded to past environmental change. In the northern hemisphere, interest is increasing in how species responded to changes in ice coverage and temperature during the last glaciation maximum (LGM, between 18000–21000 yr ago) with a common assumption that glacial refugia were located at the southern edge of a species range. Methods: We reconstructed the glacial and postglacial phylogeography of Sabatia kennedyana,...

Worldwide evidence of a unimodal relationship between productivity and plant species richness

Lauchlan H. Fraser, Jason Pither, Anke Jentsch, Marcelo Sternberg, Martin Zobel, Diana Askarizadeh, Sandor Bartha, Carl Beierkuhnlein, Jonathan A. Bennett, Alex Bittel, Bazartseren Boldgiv, Ilsi I. Boldrini, Edward Bork, Leslie Brown, Marcelo Cabido, James Cahill, Cameron N. Carlyle, Giandiego Campetella, Stefano Chelli, Ofer Cohen, Anna-Maria Csergo, Sandra Diaz, Lucas Enrico, David Ensing, Alessandra Fidelis … & Szilárd Szentes
The search for predictions of species diversity across environmental gradients has challenged ecologists for decades. The humped-back model (HBM) suggests that plant diversity peaks at intermediate productivity; at low productivity few species can tolerate the environmental stresses, and at high productivity a few highly competitive species dominate. Over time the HBM has become increasingly controversial, and recent studies claim to have refuted it. Here, by using data from coordinated surveys conducted throughout grasslands worldwide and...

Data from: Topology of tree-mycorrhizal fungus interaction networks in xeric and mesic Douglas-fir forests

Kevin J. Beiler, Suzanne W. Simard & Daniel M. Durall
1. From the phytocentric perspective, a mycorrhizal network (MN) is formed when the roots of two or more plants are colonized by the same fungal genet. MNs can be modelled as interaction networks with plants as nodes and fungal genets as links. The potential effects of MNs on facilitation or competition between plants are increasingly recognized, but their network topologies remain largely unknown. This information is needed to understand the ecological significance of MN functional...

Data from: The evolutionary history of ferns inferred from 25 low-copy nuclear genes

Carl J. Rothfels, Fay-Wei Li, Erin M. Sigel, Layne Huiet, Anders Larsson, Dylan O. Burge, Markus Ruhsam, Michael Deyholos, Douglas E. Soltis, , Shane W. Shaw, Lisa Pokorny, Tao Chen, Claude DePamphilis, Lisa DeGironimo, Li Chen, Xiaofeng Wei, Xiao Sun, Petra Korall, Dennis W. Stevenson, Sean W. Graham, Gane Ka-Shu Wong, Kathleen M. Pryer, C. Neal Stewart, Gane K-S. Wong … & Claude De Pamphilis
Premise of the study: Understanding fern (monilophyte) phylogeny and its evolutionary timescale is critical for broad investigations of the evolution of land plants, and for providing the point of comparison necessary for studying the evolution of the fern sister group, seed plants. Molecular phylogenetic investigations have revolutionized our understanding of fern phylogeny, however, to date, these studies have relied almost exclusively on plastid data. Methods: Here we take a curated phylogenomics approach to infer the...

Data from: Colonization history, host distribution, anthropogenic influence and landscape features shape populations of white pine blister rust, an invasive alien tree pathogen

Simren Brar, Clement K. M. Tsui, Braham Dhillon, Marie-Josée Bergeron, David L. Joly, P. J. Zambino, Yousry A. El-Kassaby & Richard C. Hamelin
White pine blister rust is caused by the fungal pathogen Cronartium ribicola J.C. Fisch (Basidiomycota, Pucciniales). This invasive alien pathogen was introduced into North America at the beginning of the 20th century on pine seedlings imported from Europe and has caused serious economic and ecological impacts. In this study, we applied a population and landscape genetics approach to understand the patterns of introduction and colonization as well as population structure and migration of C. ribicola....

Data from: Flowering time of butterfly nectar food plants is more sensitive to temperature than the timing of butterfly adult flight

Heather M. Kharouba & Mark Vellend
1. Variation among species in their phenological responses to temperature change suggests that shifts in the relative timing of key life cycle events between interacting species are likely to occur under climate warming. However, it remains difficult to predict the prevalence and magnitude of these shifts given that there have been few comparisons of phenological sensitivities to temperature across interacting species. 2. Here, we used a broad-scale approach utilizing collection records to compare the temperature...

Data from: Post-glacial recolonization of the North American Arctic by Arctic char (Salvelinus alpinus): genetic evidence of multiple northern refugia and hybridization between glacial lineages

Jean-Sébastien Moore, Robert Bajno, James D. Reist & Eric B. Taylor
Aims: We investigated post-glacial recolonization of the North American Arctic by Arctic char (Salvelinus alpinus) and examined potential hybridization between different glacial lineages upon secondary contact. Location: North American Arctic and adjacent areas. Methods: We collected mtDNA sequence data from 1355 individuals from 110 sampling locations and data from nine microsatellite loci from 931 individuals from 37 locations. We assessed the phylogenetic relationships and geographical distribution of mtDNA haplotypes and conducted historical demographic analyses. We...

Data from: Resources alter the structure and increase stochasticity in bromeliad microfauna communities

Jana S. Petermann, Pavel Kratina, Nicolas A. C. Marino, A. Andrew M. MacDonald, Diane S. Srivastava & Nicholas A. C. Marino
Although stochastic and deterministic processes have been found to jointly shape structure of natural communities, the relative importance of both forces may vary across different environmental conditions and across levels of biological organization. We tested the effects of abiotic environmental conditions, altered trophic interactions and dispersal limitation on the structure of aquatic microfauna communities in Costa Rican tank bromeliads. Our approach combined natural gradients in environmental conditions with experimental manipulations of bottom-up interactions (resources), top-down...

Data from: Time to get moving: assisted gene flow of forest trees

Sally N. Aitken & Jordan B. Bemmels
Geographic variation in trees has been investigated since the mid-18th century. Similar patterns of clinal variation have been observed along latitudinal and elevational gradients in common garden experiments for many temperate and boreal species. These studies convinced forest managers that a ‘local is best’ seed source policy was usually safest for reforestation. In recent decades, experimental design, phenotyping methods, climatic data and statistical analyses have improved greatly and refined but not radically changed knowledge of...

Registration Year

  • 2015

Resource Types

  • Dataset


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