49 Works

Data from: Multi-speed genome diploidization and diversification after an ancient allopolyploidization

Terezie Mandáková, Milan Pouch, Klára Harmanová, Shing Hei Zhan, Itay Mayrose & Martin A. Lysak
Hybridization and genome doubling (allopolyploidy) have led to evolutionary novelties as well as to the origin of new clades and species. Despite the importance of allopolyploidization, the dynamics of post-polyploid diploidization (PPD) at the genome level has been only sparsely studied. The Microlepidieae (MICR) is a crucifer tribe of 17 genera and c. 56 species endemic to Australia and New Zealand. Our phylogenetic and cytogenomic analyses revealed that MICR originated via an inter-tribal hybridization between...

Data from: Keeping pace with the Red Queen: identifying the genetic basis of susceptibility to infectious disease

Ailene MacPherson, Sarah P. Otto & Scott L. Nuismer
Genome-wide association studies are widely used to identify "disease genes" conferring resistance/susceptibility to infectious diseases. Using a combination of mathematical models and simulations we demonstrate that genetic interactions between hosts and parasites (GxG interactions) can drastically affect the results of these association scans and hamper our ability to detect genetic variation in susceptibility. When hosts and parasites coevolve, these GxG interactions often make Genome-wide association studies unrepeatable over time or across host populations. Reanalyzing previously...

Data from: Asymmetric competition impacts evolutionary rescue in a changing environment

Courtney L. Van Den Elzen, Elizabeth J. Kleynhans & Sarah P. Otto
Interspecific competition can strongly influence the evolutionary response of a species to a changing environment, impacting the chance that the species survives or goes extinct. Previous work has shown that when two species compete for a temporally shifting resource distribution, the species lagging behind the resource peak is the first to go extinct due to competitive exclusion. However, this work assumed symmetrically distributed resources and competition. Asymmetries can generate differences between species in population sizes,...

Data from: No evidence of inbreeding depression in sperm performance traits in wild song sparrows

Sylvain Losdat, Ryan R. Germain, Pirmin Nietlisbach, Peter Arcese & Jane M. Reid
Inbreeding is widely hypothesized to shape mating systems and population persistence, but such effects will depend on which traits show inbreeding depression. Population and evolutionary consequences could be substantial if inbreeding decreases sperm performance and hence decreases male fertilisation success and female fertility. However, the magnitude of inbreeding depression in sperm performance traits has rarely been estimated in wild populations experiencing natural variation in inbreeding. Further, the hypothesis that inbreeding could increase within-ejaculate variation in...

Data from: Decreases in beetle body size linked to climate change and warming temperatures

Michelle Tseng, Katrina M. Kaur, Sina Soleimani Pari, Karnjit Sarai, Denessa Chan, Christine H. Yao, Paula Porto, Anmol Toor, Harpawantaj S. Toor, Katrina Fograscher & Sina Soleimani Pari
1. Body size is a fundamental ecological trait and is correlated with population dynamics, community structure and function, and ecosystem fluxes. Laboratory data from broad taxonomic groups suggest that a widespread response to a warming world may be an overall decrease in organism body size. However, given the myriad of biotic and abiotic factors that can also influence organism body size in the wild, it is unclear whether results from these laboratory assays hold in...

Data from: Co-occurrence of related asexual, but not sexual, lineages suggests that reproductive interference limits coexistence

Jeannette Whitton, Christopher J. Sears & Wayne P. Maddison
We used randomizations to analyse patterns of co-occurrence of sexual and apomictic (asexual) members of the North American Crepis agamic complex (Asteraceae). We expect strong asymmetry in reproductive interactions in Crepis: apomicts produce clonal seeds with no need for pollination and are not subject to reproductive interference from co-occurring relatives. However, because they still produce some viable pollen, apomicts can reduce reproductive success of nearby sexual relatives, potentially leading to eventual local exclusion of sexuals....

Data from: Grow with the flow: a latitudinal cline in physiology is associated with more variable precipitation in Erythranthe cardinalis

Christopher D. Muir, Amy L. Angert, C. D. Muir & A. L. Angert
Local adaptation is commonly observed in nature: organisms perform well in their natal environment, but poorly outside it. Correlations between traits and latitude, or latitudinal clines, are among the most common pieces of evidence for local adaptation, but identifying the traits under selection and the selective agents is challenging. Here, we investigated a latitudinal cline in growth and photosynthesis across 16 populations of the perennial herb Erythranthe cardinalis (Phrymaceae). Using machine learning methods, we identify...

Data from: Assessing the potential of genotyping-by-sequencing-derived single nucleotide polymorphisms to identify the geographic origins of intercepted gypsy moth (Lymantria dispar) specimens: a proof-of-concept study

Sandrine Picq, Melody Keena, Nathan Havill, Don Stewart, Esther Pouliot, Brian Boyle, Roger C. Levesque, Richard C. Hamelin & Michel Cusson
Forest invasive alien species are a major threat to ecosystem stability and can have enormous economic and social impacts. For this reason, preventing the introduction of Asian gypsy moths (AGM; Lymantria dispar asiatica and L. d. japonica) into North America has been identified as a top priority by North American authorities. The AGM is an important defoliator of a wide variety of hardwood and coniferous trees, displaying a much broader host range and an enhanced...

Data from: Theory, practice, and conservation in the age of genomics: the Galápagos giant tortoise as a case study

Stephen J. Gaughran, Maud C. Quinzin, Joshua M. Miller, Ryan C. Garrick, Danielle L. Edwards, Michael A. Russello, Nikos Poulakakis, Claudio Ciofi, Luciano B. Beheregaray, Aldalgisa Caccone & Adalgisa Caccone
Hgh-throughput DNA sequencing allows efficient discovery of thousands of single nucleotide polymorphisms (SNPs) in non-model species. Population genetic theory predicts that this large number of independent markers should provide detailed insights into population structure, even when only a few individuals are sampled. Still, sampling design can have a strong impact on such inferences. Here, we use simulations and empirical SNP data to investigate the impacts of sampling design on estimating genetic differentiation among populations that...

Data from: Genetic coupling of female mate choice with polygenic ecological divergence facilitates stickleback speciation

Rachael A. Bay, Matthew E. Arnegard, Gina L. Conte, Jacob Best, Nicole L. Bedford, Shaugnessy R. McCann, Matthew E. Dubin, Yingguang Frank Chan, Felicity C. Jones, David M. Kingsley, Dolph Schluter & Catherine L. Peichel
Ecological speciation with gene flow is widespread in nature, but it presents a conundrum: how are associations between traits under divergent natural selection and traits that contribute to assortative mating maintained? Theoretical models suggest that genetic mechanisms inhibiting free recombination between loci underlying these two types of traits (hereafter, “genetic coupling”) can facilitate speciation. Here, we perform a direct test for genetic coupling by mapping both divergent traits and female mate choice in a classic...

Data from: Density-dependent signaling: an alternative hypothesis on the function of chemical signaling in a non-territorial solitary carnivore

Clayton T. Lamb, Garth Mowat, Sophie L. Gilbert, Bruce N. McLellan, Scott E. Nielsen & Stan Boutin
Brown bears are known to use rubbing behavior as a means of chemical communication, but the function of this signaling is unclear. One hypothesis that has gained support is that male bears rub to communicate dominance to other males. We tested the communication of dominance hypothesis in a low-density brown bear population in southeast British Columbia. We contrasted rubbing rates for male and female bears during and after the breeding season using ten years of...

Data from: A genome-wide phylogeny of jumping spiders (Araneae, Salticidae), using anchored hybrid enrichment

Wayne P. Maddison, Samuel C. Evans, Chris A. Hamilton, Jason E. Bond, Alan R. Lemmon & Emily Moriarty Lemmon
We present the first genome-wide molecular phylogeny of jumping spiders (Araneae: Salticidae), inferred from Anchored Hybrid Enrichment (AHE) sequence data. From 12 outgroups plus 34 salticid taxa representing all but one subfamily and most major groups recognized in previous work, we obtained 447 loci totalling 96,946 aligned nucleotide sites. Our analyses using concatenated likelihood, parsimony, and coalescent methods (ASTRAL and SVDQuartets) strongly confirm most previous results, resolving as monophyletic the Spartaeinae, Salticinae (with the hisponines...

Data from: Linking the wintering and breeding grounds of warblers along the Pacific Flyway

David P. L. Toews, Julian Heavyside & Darren E. Irwin
Long-distance migration is a behavior that is exhibited by many animal groups. The evolution of novel migration routes can play an important role in range expansions, ecological interactions, and speciation. New migration routes may evolve in response to selection in favor of reducing distance between breeding and wintering areas, or avoiding navigational barriers. Many migratory changes are likely to evolve gradually and are therefore difficult to study. Here, we attempt to connect breeding and wintering...

Data from: Using experimentation to understand the 10-year snowshoe hare cycle in the boreal forest of North America

Charles Krebs, Rudy Boonstra, Stan Boutin & Charles J. Krebs
1. Population cycles have long fascinated ecologists from the time of Charles Elton in the 1920s. The discovery of large population fluctuations in undisturbed ecosystems challenged the idea that pristine nature was in a state of balance. The 10-year cycle of snowshoe hares (Lepus americanus Erxleben) across the boreal forests of Canada and Alaska is a classic cycle, recognized by fur traders for more than 300 years. 2. Since the 1930s ecologists have investigated the...

Data from: Novel predators reshape holozoan phylogeny and reveal the presence of a two-component signalling system in the ancestor of animals

Elisabeth Hehenberger, Denis V. Tikhonenkov, Martin Kolisko, Javier Del Campo, Anton S. Esaulov, Alexander P. Mylnikov & Patrick J. Keeling
Our understanding of the origin of animals has been transformed by characterizing their most closely related, unicellular sisters: the choanoflagellates, filastereans, and ichthyosporeans. Together with animals, these lineages make up the Holozoa [ 1, 2 ]. Many traits previously considered “animal specific” were subsequently found in other holozoans [ 3, 4 ], showing that they evolved before animals, although exactly when is currently uncertain because several key relationships remain unresolved [ 2, 5 ]. Here...

Data from: Gene expression plasticity in response to salinity acclimation in threespine stickleback ecotypes from different salinity habitats

Taylor C. Gibbons, David C. H. Metzger, Timothy M. Healy & Patricia M. Schulte
Phenotypic plasticity is thought to facilitate the colonization of novel environments and shape the direction of evolution in colonizing populations. However, the relative prevalence of various predicted patterns of changes in phenotypic plasticity following colonization remain unclear. Here we use a whole-transcriptome approach to characterize patterns of gene expression plasticity in the gills of a freshwater-adapted and a saltwater-adapted ecotype of threespine stickleback (Gasterosteus aculeatus) exposed to a range of salinities. The response of the...

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: Genetic and genomic evidence of niche partitioning and adaptive radiation in mountain pine beetle fungal symbionts

Dario I. Ojeda Alayon, Clement K. M. Tsui, Nicolas Feau, Arnaud Capron, Braham Dhillon, Zhang Yiyuan, Sepideh Massoumi Alamouti, Celia K. Boone, Allan L. Carroll, Janice E.K. Cooke, Amanda D. Roe, Felix A. H. Sperling, Richard C. Hamelin, Janice E. K. Cooke & Yiyuan Zhang
Bark beetles form multipartite symbiotic associations with blue stain fungi (Ophiostomatales, Ascomycota). These fungal symbionts play an important role during the beetle's life cycle by providing nutritional supplementation, overcoming tree defences and modifying host tissues to favour brood development. The maintenance of stable multipartite symbioses with seemingly less competitive symbionts in similar habitats is of fundamental interest to ecology and evolution. We tested the hypothesis that the coexistence of three fungal species associated with the...

Data from: Dispersal barriers and climate determine the geographic distribution of the helicopter damselfly Mecistogaster modesta

Sarah L. Amundrud, Martin Videla & Diane S. Srivastava
Species’ ranges are typically constrained by the interplay of physical barriers to dispersal, environmental requirements such as suitable climatic conditions and biotic constraints such as from predation or competition. However, teasing apart the relative importance of these constraints in determining species distributions still represents a major challenge for ecologists. The Neotropical damselfly Mecistogaster modesta (Coenagrionidae: Odonata) inhabits wet and moist forests in mainland Central America and north-western South America. This habitat specialist spends its larval...

Data from: Using fuzzy logic to determine the vulnerability of marine species to climate change

Miranda C. Jones & William W. L. Cheung
Marine species are being impacted by climate change and ocean acidification, although their level of vulnerability varies due to differences in species' sensitivity, adaptive capacity and exposure to climate hazards. Due to limited data on the biological and ecological attributes of many marine species, as well as inherent uncertainties in the assessment process, climate change vulnerability assessments in the marine environment frequently focus on a limited number of taxa or geographic ranges. As climate change...

Data from: Group elicitations yield more consistent, yet more uncertain experts in understanding risks to ecosystem services in New Zealand bays

Gerald G. Singh, Jim Sinner, Joanne Ellis, Milind Kandlikar, Benjamin S. Halpern, Terre Satterfield & Kai Chan
The elicitation of expert judgment is an important tool for assessment of risks and impacts in environmental management contexts, and especially important as decision-makers face novel challenges where prior empirical research is lacking or insufficient. Evidence-driven elicitation approaches typically involve techniques to derive more accurate probability distributions under fairly specific contexts. Experts are, however, prone to overconfidence in their judgements. Group elicitations with diverse experts can reduce expert overconfidence by allowing cross-examination and reassessment of...

Data from: Aggressive behaviours, food deprivation and the foraging gene

Silu Wang & Marla B. Sokolowski
A pleiotropic gene governs multiple traits, which might constrain the evolution of complexity due to conflicting selection on these traits. However, if the pleiotropic effect is modular, then this can facilitate synergistic responses to selection on functionally related traits, thereby leveraging the evolution of complexity. To understand the evolutionary consequence of pleiotropy, the relation among functionally different traits governed by the same gene is key. We examined a pleiotropic function of the foraging (for) gene...

Data from: Estimations of evapotranspiration in an age sequence of Eucalyptus plantations in subtropical China

Wenfei Liu, Jianping Wu, Houbao Fan, Honglang Duan, Qiang Li, Yinghong Yuan & Hao Zhang
Eucalyptus species are widely planted for reforestation in subtropical China. However, the effects of Eucalyptus plantations on the regional water use remain poorly understood. In an age sequence of 2-, 4- and 6-year-old Eucalyptus plantations, the tree water use and soil evaporation were examined by linking model estimations and field observations. Results showed that annual evapotranspiration of each age sequence Eucalyptus plantations was 876.7, 944.1 and 1000.7 mm, respectively, accounting for 49.81%, 53.64% and 56.86%...

Data from: Genetic sampling for estimating density of common species

Ellen Cheng, Karen E. Hodges, Rahel Sollmann & L. Scott Mills
Understanding population dynamics requires reliable estimates of population density, yet this basic information is often surprisingly difficult to obtain. With rare or difficult-to-capture species, genetic surveys from noninvasive collection of hair or scat has proved cost-efficient for estimating densities. Here, we explored whether noninvasive genetic sampling (NGS) also offers promise for sampling a relatively common species, the snowshoe hare (Lepus americanus Erxleben, 1777), in comparison with traditional live trapping. We optimized a protocol for single-session...

Data from: Light and growth form interact to shape stomatal ratio among British angiosperms

Christopher D. Muir
In most plants, stomata are located only on the abaxial leaf surface (hypostomy), but many plants have stomata on both surfaces (amphistomy). High light and herbaceous growth form have been hypothesized to favor amphistomy, but these hypotheses have not been rigorously tested together using phylogenetic comparative methods. I leveraged a large dataset including stomatal ratio, Ellenberg light indicator value, growth form and phylogenetic relationships for 372 species of British angiosperms. I used phylogenetic comparative methods...

Registration Year

  • 2017

Resource Types

  • Dataset


  • University of British Columbia
  • University of Toronto
  • University of Montana
  • University of California System
  • University of Alberta
  • University of Calgary
  • Universiti of Malaysia Sabah
  • Fujian Agriculture and Forestry University
  • Tel Aviv University
  • Université Laval
  • Universiti Malaysia Sarawak
  • Cornell University
  • College of Charleston
  • Nanchang Institute of Technology
  • University of Washington