28 Works

Data from: The adaptive potential of Populus balsamifera L. to phenology requirements in a warmer global climate

Matthew S. Olson, Nicholas Levsen, Raju Y. Soolanayakanahally, Robert D. Guy, William R. Schroeder, Stephen R. Keller & Peter Tiffin
The manner in which organisms adapt to climate change informs both a broader understanding of the evolution of biodiversity as well as plans for future conservation and mitigation. We apply common garden and association mapping approaches to quantify genetic variance and identify loci affecting bud flush and bud set, traits that define a tree’s season for height growth, in the boreal forest tree Populus balsamifera L. (balsam poplar). Using data from 478 genotypes grown in...

Data from: The population genomics of sunflowers and genomic determinants of protein evolution revealed by RNAseq

Sébastien Renaut, Christopher J. Grassa, Brook T. Moyers, Nolan C. Kane, Loren H. Rieseberg, Christopher Grassa, Brook Moyers, Nolan Kane & Loren Rieseberg
Few studies have investigated the causes of evolutionary rate variation among plant nuclear genes, especially in recently diverged species still capable of hybridizing in the wild. The recent advent of Next Generation Sequencing (NGS) permits investigation of genome wide rates of protein evolution and the role of selection in generating and maintaining divergence. Here, we use individual whole-transcriptome sequencing (RNAseq) to refine our understanding of the population genomics of a wild species of sunflowers (Helianthus...

Data from: Rat aversion to isoflurane versus carbon dioxide

Devina Wong, I. Joanna Makowska, Weary M. Weary & D. M. Weary
Some experts suggest that sedation of laboratory rodents with isoflurane before euthanasia with carbon dioxide (CO2) is a humane alternative to euthanasia with CO2 alone, but little research has compared aversion to these agents. Albino rats were tested in a light/dark box where they had the choice between remaining in a dark compartment filling with isoflurane or CO2, or escaping to a lit compartment. Experiment 1 validated the procedure by confirming that rats responded to...

Data from: Multilocus estimation of selfing and its heritability

Nathan S. McClure & Michael C. Whitlock
We describe a new method of estimating the selfing rate (S) in a mixed mating population based on a population structure approach that accounts for possible intergenerational correlation in selfing rate, giving rise to an estimate of the upper limit for heritability of selfing rate (h^2). A correlation between generations in selfing rate is shown to affect one- and two-locus probabilities of identity by descent. Conventional estimates of selfing rate based on a population structure...

Data from: Detecting small-scale genotype-environment interactions in apomictic dandelion (Taraxacum officinale) populations

Kylie A. McLeod, Moira Scascitelli & Mark Vellend
Studies of genotype × environment interactions (G×E) and local adaptation provide critical tests of natural selection’s ability to counter opposing forces such as gene flow. Such studies may be greatly facilitated in asexual species, given the possibility for experimental replication at the level of true genotypes (rather than populations) and the possibility of using molecular markers to assess genotype-environment associations in the field (neither of which is possible for most sexual species). Here we tested...

Data from: Oceanographic drivers of offspring abundance may increase or decrease variance in reproductive success in a temperate marine fish

Katie E. Lotterhos & Russell W. Markel
In species that reproduce into uncertain environments, the relationship between mean reproductive success (the abundance of new recruits) and the variance in reproductive success (whether adults contribute disproportionally more offspring) may not be straightforward because of stochastic environmental processes that create high variance in reproductive success among adults. In this study we investigated the relationships between oceanography, reproductive success, and reproductive variance in the black rockfish, Sebastes melanops, a long-lived temperate reef fish with pelagic...

Data from: Recent non-hybrid origin of sunflower ecotypes in a novel habitat

Loren H. Rieseberg, Rose L. Andrew, Nolan C. Kane, Greg J. Baute & Christopher J. Grassa
The genomics of local adaptation is an increasingly active field, providing insights into the forces driving ecological speciation and the repeatability of evolution. Demography and gene flow play an important role in determining the paths by which parallel evolution occurs and the genomic signatures of adaptation. In the annual sunflowers, hybridization between species has repeatedly led to the colonization of extreme habitats, such as sand dunes. In a new case of adaptation to sand dunes...

Data from: Diverse reproductive barriers in hybridising crickets suggests extensive variation in the evolution and maintenance of isolation

Thor Veen, Joseph Faulks, Frances Tyler, Jodie Lloyd & Tom Tregenza
Reproductive barriers reduce gene flow between populations and maintain species identities. A diversity of barriers exist, acting before, during and after mating. To understand speciation and coexistence, these barriers need to be quantified and their potential interactions revealed. We use the hybridising field crickets Gryllus bimaculatus and G. campestris as a model to understand the full compliment and relative strength of reproductive barriers. We find that males of both species prefer conspecific females, but the...

Data from: Phylogenetic conservatism in plant phenology

T. Jonathan Davies, Elizabeth M. Wolkovich, Nathan J. B. Kraft, Nicolas Salamin, Jenica M. Allen, Toby R. Ault, Julio L. Betancourt, Kjell Bolmgren, Elsa E. Cleland, Benjamin I. Cook, Theresa M. Crimmins, Susan J. Mazer, Gregory J. McCabe, Stephanie Pau, Jim Regetz, Mark D. Schwartz & Steven E. Travers
Phenological events – defined points in the life cycle of a plant or animal – have been regarded as highly plastic traits, reflecting flexible responses to various environmental cues. The ability of a species to track, via shifts in phenological events, the abiotic environment through time might dictate its vulnerability to future climate change. Understanding the predictors and drivers of phenological change is therefore critical. Here, we evaluated evidence for phylogenetic conservatism – the tendency...

Data from: Coexistence and origin of trophic ecotypes of pygmy whitefish, Prosopium coulterii, in southwestern Alaskan lake

Tom P. Quinn, Conrad P. Gowell & Eric B. Taylor
Ecologically, morphologically, and genetically distinct populations within single taxa often co-exist in postglacial lakes and have provided important model systems with which to investigate ecological and evolutionary processes such as niche partitioning and ecological speciation. Within the Salmonidae, these species complexes have been well studied, particularly within the Coregonus clupeaformis-C. laveratus (lake and European whitefish, respectively) group, but the phenomenon has been less well documented in the other whitefish genera, Prosopium and Stenodus. Here, we...

Data from: Extra-pair paternity and the variance in male fitness in song sparrows (Melospiza melodia)

Christophe Lebigre, Peter Arcese, Rebecca J. Sardell, Lukas F. Keller & Jane M. Reid
The variance in fitness across population members can influence major evolutionary processes. In socially monogamous but genetically polygynandrous species, extra-pair paternity (EPP) is widely hypothesized to increase the variance in male fitness compared to that arising given the socially monogamous mating system. This hypothesis has not been definitively tested because comprehensive data describing males’ apparent (social) and realized (genetic) fitness have been lacking. We used 16 years of comprehensive social and genetic paternity data for...

Data from: Multiple post-mating barriers to hybridisation in field crickets

Frances Tyler, Xavier A. Harrison, Amanda Bretman, Thor Veen, Rolando Rodríguez-Muñoz & Tom Tregenza
Mechanisms that prevent different species from interbreeding are fundamental to the maintenance of biodiversity. Barriers to interspecific matings, such as failure to recognize a potential mate, are often relatively easy to identify. Those occurring after mating, such as differences in the how successful sperm are in competition for fertilisations, are cryptic and have the potential to create selection on females to mate multiply as a defence against maladaptive hybridization. Cryptic advantages to conspecific sperm may...

Data from: The red queen coupled with directional selection favors the evolution of sex

Emma E. Hodgson & Sarah P. Otto
Why sexual reproduction has evolved to be such a widespread mode of reproduction remains a major question in evolutionary biology. While previous studies have shown that increased sex and recombination can evolve in the presence of host-parasite interactions (the “Red Queen hypothesis” for sex), many of these studies have assumed that multiple loci mediate infection versus resistance. Data suggest, however, that a major locus is typically involved in antigen presentation and recognition. Here, we explore...

Data from: The maintenance of obligate sex in finite, structured populations subject to recurrent beneficial and deleterious mutation

Matthew Hartfield, Sarah P. Otto & Peter David Keightley
Although there is no known general explanation as to why sexual populations resist asexual invasion, previous work has shown that sexuals can outcompete asexuals in structured populations. However, it is currently unknown whether costly sex can be maintained with the weak structure that is commonly observed in nature. We investigate the conditions under which obligate sexuals resist asexual invasion in structured populations subject to recurrent mutation. We determine the level of population structure needed to...

Data from: Refining the conditions for sympatric ecological speciation

Florence Débarre
Can speciation occur in a single population when different types of resources are available, in the absence of any geographical isolation, or any spatial or temporal variation in selection? The controversial topics of sympatric speciation and ecological speciation have already stimulated many theoretical studies, most of them agreeing on the fact that mechanisms generating disruptive selection, some level of assortment, and enough heterogeneity in the available resources, are critical for sympatric speciation to occur. Few...

Data from: Development of an ultra-dense genetic map of the sunflower genome

John E. Bowers, Savithri Nambeesan, Jonathan Corbi, John M. Burke, Michael S. Barker, Loren H. Rieseberg & Steven J. Knapp
The development of ultra-dense genetic maps has the potential to facilitate detailed comparative genomic analyses and whole genome sequence assemblies. Here we describe the use of a custom Affymetrix GeneChip containing nearly 2.4 million features (25 bp sequences) targeting 86,023 unigenes from sunflower (Helianthus annuus L.) and related species to test for single-feature polymorphisms (SFPs) in a recombinant inbred line (RIL) mapping population derived from a cross between confectionery and oilseed sunflower lines (RHA280 x...

Data from: Genomic and phenotypic architecture of a spruce hybrid zone (Picea sitchensis x P. glauca)

Jill A. Hamilton, Christian Lexer & Sally N. Aitken
Interspecific hybridization may enhance the capacity of populations to adapt to changing environments, and has practical implications for reforestation. We use genomewide estimates of admixture and phenotypic traits for trees in a common garden to examine the extent and direction of gene flow across a Picea hybrid zone, testing assumptions of the bounded hybrid superiority and tension zone models of hybrid zone maintenance. Seeds were collected from the ecological transition zone spanning from maritime to...

Data from: Vertical partitioning between sister species of Rhizopogon fungi on mesic and xeric sites in an interior Douglas-fir forest

Kevin J. Beiler, Suzanne W. Simard, Valerie LeMay & Daniel M. Durall
Understanding ectomycorrhizal fungal (EMF) community structure is limited by a lack of taxonomic resolution and autecological information. Rhizopogon vesiculosus and R. vinicolor (Basidiomycota) are morphologically and genetically related species. They are dominant members of interior Douglas-fir (Pseudotsuga menziesii var. glauca) EMF communities, but mechanisms leading to their coexistence are unknown. We investigated the microsite associations and foraging strategy of individual R. vesiculosus and R. vinicolor genets. Mycelia spatial patterns, pervasiveness and root colonization patterns of...

Data from: The diet of an endemic subspecies of the Eurasian Spoonbill Platalea leucorodia balsaci, breeding at the Banc d’Arguin, Mauritania

J. Veen, Thor Veen & O. Overdijk
In the period 1998–2010 the endemic subspecies of the Eurasian Spoonbill Platalea leucorodia balsaci breeding in Mauritania has decreased in numbers considerably. The causes for this decline are unknown. This study aimed to investigate the diet of the species. We analysed faecal material collected in the breeding colonies in 8 different years. The results show that Mauritanian Spoonbills almost exclusively eat shrimp (59.7%) and small fish (35.4%), the latter being dominated by Gobiidae (20.8%), Soleidae...

Data from: Population genomics of Pacific lamprey: adaptive variation in a highly dispersive species

Jon E. Hess, Nathan R. Campbell, David A. Close, Margaret F. Docker & Shawn R. Narum
Unlike most anadromous fishes that have evolved strict homing behaviour, Pacific lamprey (Entosphenus tridentatus) seem to lack philopatry as evidenced by minimal population structure across the species range. Yet unexplained findings of within-region population genetic heterogeneity coupled with the morphological and behavioural diversity described for the species suggest that adaptive genetic variation underlying fitness traits may be responsible. We employed restriction site–associated DNA sequencing to genotype 4439 quality filtered single nucleotide polymorphism (SNP) loci for...

Data from: Experimental confirmation that body size determines mate preference via phenotype matching in a stickleback species pair

Gina L. Conte & Dolph Schluter
Mate choice by phenotype matching, whereby individuals prefer a mate whose phenotype is similar to their own, should facilitate speciation with gene flow. This is because the genes that control mate signal (the phenotype being matched) also determine the preferred mate signal (‘mate preference’). Speciation is made even easier if phenotype matching is based on a trait under divergent natural selection. In this case, assortative mating should readily evolve as a by-product of divergent selection...

Data from: Genetic signature of adaptive peak shift in threespine stickleback

Sean M. Rogers, Patrick Tamkee, Brian Summers, Sarita Balabahadra, Melissa Marks, David E. Kingsley & Dolph Schluter
Transition of an evolving population to a new adaptive optimum is predicted to leave a signature in the distribution of effect sizes of fixed mutations. If they affect many traits (are pleiotropic), large effect mutations should contribute more when a population evolves to a farther adaptive peak than to a nearer peak. We tested this prediction in wild threespine stickleback fish (Gasterosteus aculeatus) by comparing the estimated frequency of large effect genetic changes underlying evolution...

Data from: Mandated data archiving greatly improves access to research data

Timothy H. Vines, Rose L. Andrew, Dan G. Bock, Michelle T. Franklin, Kimberly J. Gilbert, Nolan C. Kane, Jean-Sébastien Moore, Brook T. Moyers, Sébastien Renaut, Diana J. Rennison, Thor Veen & Sam Yeaman
The data underlying scientific papers should be accessible to researchers both now and in the future, but how best can we ensure that these data are available? Here we examine the effectiveness of four approaches to data archiving: no stated archiving policy, recommending (but not requiring) archiving, and two versions of mandating data deposition at acceptance. We control for differences between data types by trying to obtain data from papers that use a single, widespread...

Data from: Mandible allometry in extant and fossil Balaenopteridae (Cetacea: Mammalia): the largest vertebrate skeletal element and its role in rorqual lunge-feeding

Nicholas D. Pyenson, Jeremy A. Goldbogen & Robert E. Shadwick
Rorqual whales (crown Balaenopteridae) are unique among aquatic vertebrates in their ability to lunge-feed. During a single lunge, rorquals rapidly engulf a large volume of prey-laden water at high speed, which they then filter to capture suspended prey. Engulfment biomechanics are mostly governed by the coordinated opening and closing of the mandibles at large gape angles, which differentially exposes the floor of the oral cavity to oncoming flow. Mouth area in rorquals is delimited by...

Data from: Mutational effects depend on ploidy level: all else is not equal

Aleeza C. Gerstein
Ploidy is predicted to influence adaptation directly, yet whether single mutations behave the same in different ploidy backgrounds has not been well studied. It has often been assumed theoretically that aside from dominance, selective parameters do not differ between cells of varying ploidy. Using the budding yeast Saccharomyces cerevisiae, I compared the effect size of 20 adaptive mutations in haploids and homozygous diploids and found, surprisingly, that the same mutations often had a much larger...

Registration Year

  • 2012

Resource Types

  • Dataset


  • University of British Columbia
  • University of California, San Diego
  • Indiana University Bloomington
  • University of Exeter
  • University of Maryland, College Park
  • Florida State University
  • Swiss Institute of Bioinformatics
  • University of Washington
  • Stanford University
  • University of Georgia