22 Works

Data from: Geographical barriers and climate influence demographic history in narrowleaf cottonwoods

Luke M. Evans, Gerard J. Allan, Stephen P. DiFazio, Gancho T. Slavov, Jason A. Wilder, Kevin D. Floate, Stewart B. Rood & Thomas G. Whitham
Studies of genetic variation can clarify the role of geography and spatio-temporal variation of climate in shaping demography, particularly in temperate zone tree species with large latitudinal ranges. Here, we examined genetic variation in narrowleaf cottonwood, Populus angustifolia, a dominant riparian tree. Using multi-locus surveys of polymorphism in 363 individuals across the species’ 1800 km latitudinal range, we found that, first, P. angustifolia has stronger neutral genetic structure than many forest trees (simple sequence repeat...

Data from: An evolutionary modelling approach to understanding the factors behind plant invasiveness and community susceptibility to invasion

John Warren, Chris J Topping & Penri James
Ecologists have had limited success in understanding which introduced species may become invasive. An evolutionary model is used to investigate which traits are associated with invasiveness. Translocation experiments were simulated in which species were moved into similar but evolutionary younger communities. The main findings were that species that had previously been the most abundant in their original communities have significantly higher rates of establishment than did species that had previously occurred at low abundance in...

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: Nonadditive changes to cytosine methylation as a consequence of hybridization and genome duplication in Senecio (Asteraceae)

Matthew J Hegarty, Tom Batstone, Gary L Barker, Keith J Edwards, Richard J Abbott & Simon J Hiscock
The merger of two or more divergent genomes within an allopolyploid nucleus can facilitate speciation and adaptive evolution in flowering plants. Widespread changes to gene expression have been shown to result from interspecific hybridisation and polyploidy in a number of plant species, and attention has now shifted to determining the epigenetic processes which drive these changes. We present here an analysis of cytosine methylation patterns in triploid F1 Senecio (ragwort) hybrids and their allohexaploid derivatives....

Data from: Floral resource partitioning by individuals within generalised hoverfly pollination networks revealed by DNA metabarcoding

Andrew Lucas, Owen Bodger, Berry J. Brosi, , Dan W. Forman, Carolyn Greig, Matthew Hegarty, Laura Jones, Penelope J. Neyland & Natasha De Vere
Pollination is a key ecosystem service for agriculture and wider ecosystem function. However, most pollination studies focus on Hymenoptera, with hoverflies (Syrphidae) frequently treated as a single functional group. We tested this assumption by investigating pollen carried by eleven species of hoverfly in five genera, Cheilosia, Eristalis, Rhingia, Sericomyia and Volucella, using DNA metabarcoding. Hoverflies carried pollen from 59 plant taxa, suggesting they visit a wider number of plant species than previously appreciated. Most pollen...

Data from: Canonical correlations reveal adaptive loci and phenotypic responses to climate in perennial ryegrass

José L. Blanco-Pastor, Philippe Barre, Thomas Keep, Thomas Ledauphin, Abraham Escobar-Gutiérrez, Anna Maria Roschanski, Evelyn Willner, Klaus Dehmer, Matthew Hegarty, Hilde Muylle, Elisabeth Veeckman, Klaas Vandepoele, Tom Ruttink, Isabel Roldán-Ruiz, Stéphanie Manel & Jean-Paul Sampoux
Germplasm from perennial ryegrass (Lolium perenne L.) natural populations is useful for breeding because of its adaptation to a wide range of climates. Climate-adaptive genes can be detected from associations between genotype, phenotype and climate but an integrated framework for the analysis of these three sources of information is lacking. We used two approaches to identify adaptive loci in perennial ryegrass and their effect on phenotypic traits. First, we combined Genome-Environment Association (GEA) and GWAS...

Data from: Best of both worlds? Association between outcrossing and parasite loads in a selfing fish

Amy Ellison, Joanne Cable & Sofia Consuegra
Mixed-mating strategies (i.e. intermediate levels of self-fertilization and outcrossing in hermaphrodites) are relatively common in plants and animals, but why self-fertilization (selfing) rates vary so much in nature has proved difficult to explain. We tested the hypothesis that parasites help maintain mixed-mating using a partially selfing fish (Kryptolebias marmoratus) as a model. We show that outcrossed progeny in the wild are genetically more diverse and less susceptible to multiple parasite infections than their selfed counterparts....

Data from: Maintaining functional major histocompatibility complex diversity under inbreeding: the case of a selfing vertebrate

A. Ellison, J. Allainguillaume, S. Girdwood, J. Pachebat, K. M. Peat, P. Wright, Sofia Consuegra Del Olmo & S. Consuegra
Major histocompatibility complex (MHC) genes encode proteins that present pathogen-derived antigens to T-cells, initiating the adaptive immune response in vertebrates. Although populations with low MHC diversity tend to be more susceptible to pathogens, some bottlenecked populations persist and even increase in numbers despite low MHC diversity. Thus, the relative importance of MHC diversity versus genome-wide variability for the long-term viability of populations after bottlenecks and/or under high inbreeding is controversial. We tested the hypothesis that...

Data from: Oxidative stress and the evolution of sex differences in lifespan and ageing in the decorated cricket, Gryllodes sigillatus

Catharine Ruth Archer, Scott K. Sakaluk, Colin Selman, Nick Royle & John Hunt
The Free Radical Theory of Ageing (FRTA) predicts that oxidative stress, induced when levels of reactive oxygen species exceed the capacity of antioxidant defences, causes ageing. Recently, it has also been argued that oxidative damage may mediate important life-history trade-offs. Here, we use inbred lines of the decorated cricket, Gryllodes sigillatus, to estimate the genetic (co)variance between age-dependent reproductive effort, lifespan, ageing, oxidative damage and total antioxidant capacity within and between the sexes. The FRTA...

Ectopic expression of Triticum polonicum VRT-A2 underlies elongated glumes and grains in hexaploid wheat in a dosage-dependent manner: Additional data (images, phylogenetic alignments and trees)

Nikolai Adamski, James Simmonds, Jemima Brinton, Anna Backhaus, Yi Chen, Mark Smedley, Sadiye Hayta, Tobin Florio, Pamela Crane, Peter Scott, Alice Pieri, Olyvia Hall, J. Elaine Barclay, Myles Clayton, John Doonan, Candida Nibau & Cristobal Uauy
Flower development is an important determinant of grain yield in crops. In wheat, natural variation for the size of spikelet and floral organs is particularly evident in Triticum polonicum, a tetraploid subspecies of wheat with long glumes, lemmas, and grains. Using map-based cloning, we identified VRT2, a MADS-box transcription factor belonging to the SVP family, as the gene underlying the P1 locus. The causal P1 mutation is a sequence substitution in intron-1 that results in...

Data from: Age, state, environment and season dependence of senescence in body mass

Svenja B. Kroeger, Daniel T. Blumstein, Kenneth B. Armitage, Jane M. Reid, Julien G.A. Martin & Julien G. A. Martin
Data file in csv formatBMdata.csvRcode

Data from: Horizontal gene flow from Eubacteria to Archaebacteria and what it means for our understanding of eukaryogenesis

Wasiu A. Akanni, Karen Siu-Ting, Christopher J. Creevey, James O. McInerney, Mark Wilkinson, Peter G. Foster & Davide Pisani
The origin of the eukaryotic cell is considered one of the major evolutionary transitions in the history of life. Current evidence strongly supports a scenario of eukaryotic origin in which two prokaryotes, an archaebacterial host and an α-proteobacterium (the free-living ancestor of the mitochondrion), entered a stable symbiotic relationship. The establishment of this relationship was associated with a process of chimerization, whereby a large number of genes from the α-proteobacterial symbiont were transferred to the...

Data from: Cell wall composition and bioenergy potential of rice straw tissues are influenced by environment, tissue type, and genotype

Paul Tanger, Miguel E. Vega-Sánchez, Margaret Fleming, Kim Tran, Seema Singh, James B. Abrahamson, Courtney E. Jahn, Nicholas Santoro, Elizabeth B. Naredo, Marietta Baraoidan, John M. C. Danku, David E. Salt, Kenneth L. McNally, Blake A. Simmons, Pamela C. Ronald, Hei Leung, Daniel R. Bush, John K. McKay & Jan E. Leach
Breeding has transformed wild plant species into modern crops, increasing the allocation of their photosynthetic assimilate into grain, fiber, and other products for human use. Despite progress in increasing the harvest index, much of the biomass of crop plants is not utilized. Potential uses for the large amounts of agricultural residues that accumulate are animal fodder or bioenergy, though these may not be economically viable without additional efforts such as targeted breeding or improved processing....

Data from: Winning the invasion roulette: escapes from fish farms increase admixture and facilitate establishment of non-native rainbow trout

Sofia Consuegra, Nia Phillips, Gonzalo Gajardo & Carlos Garcia De Leaniz
Aquaculture is a major source of invasive aquatic species, despite the fact that cultured organisms often have low genetic diversity and tend to be maladapted to survive in the wild. Yet, to what extent aquaculture escapees become established by means of high propagule pressure and multiple origins is not clear. We analysed the genetic diversity of 15 established populations and 4 farmed stocks of non-native rainbow trout in Chile, a species first introduced for recreational...

Data From: Genetic structure of recently fragmented suburban populations of European stag beetle

Karen Cox, Niall Mckeown, An Vanden Broeck, An Van Breusegem, Roger Cammaerts & Arno Thomaes
Habitat loss and fragmentation due to urbanisation can negatively affect metapopulation persistence when gene flow among populations is reduced and population sizes decrease. Inference of patterns and processes of population connectivity derived from spatial genetic analysis has proven invaluable for conservation and management. However, a more complete account of population dynamics may be obtained by combining spatial and temporal sampling. We, therefore, performed a genetic study on European stag beetle (Lucanus cervus L.) populations in...

Data from: Beak color dynamically signals changes in fasting status and parasite loads in king penguins

Quentin Schull, F. Stephen Dobson, Antoine Stier, Jean-Patrice Robin, Pierre Bize & Vincent A. Viblanc
Dynamic ornamental signals that vary over minutes, hours or weeks can yield continuous information on individual condition (e.g., energy reserves or immune status), and may therefore be under strong social and/or sexual selection. In vertebrates, the coloration of the integument is often viewed as a dynamic ornament, which in birds can be apparent in the beak. King penguins (Aptenodytes patagonicus) are monomorphic seabirds that possess conspicuous yellow–orange (YO) and ultraviolet (UV) beak spots that are...

Data from: Population structure and history of the Welsh sheep breeds determined by whole genome genotyping

Sarah E. Beynon, Gancho T. Slavov, Marta Farré, Bolormaa Sunduimijid, Kate Waddams, Brian Davies, William Haresign, James Kijas, Iona M. MacLeod, C. Jamie Newbold, Lynfa Davies & Denis M. Larkin
Background: One of the most economically important areas within the Welsh agricultural sector is sheep farming, contributing around £230 million to the UK economy annually. Phenotypic selection over several centuries has generated a number of native sheep breeds, which are presumably adapted to the diverse and challenging landscape of Wales. Little is known about the history, genetic diversity and relationships of these breeds with other European breeds. We genotyped 353 individuals from 18 native Welsh...

Data from: Transcriptomic analysis of the lesser spotted catshark (Scyliorhinus canicula) pancreas, liver and brain reveals molecular level conservation of vertebrate pancreas function

John F. Mulley, Adam D. Hargreaves, Matthew J. Hegarty, R. Scott Heller & Martin T. Swain
Background: Understanding the evolution of the vertebrate pancreas is key to understanding its functions. The chondrichthyes (cartilaginous fish such as sharks and rays) have often been suggested to possess the most ancient example of a distinct pancreas with both hormonal (endocrine) and digestive (exocrine) roles. The lack of genetic, genomic and transcriptomic data for cartilaginous fish has hindered a more thorough understanding of the molecular-level functions of the chondrichthyan pancreas, particularly with respect to their...

Data from: Winning the invasion roulette: escapes from fish farms increase admixture and facilitate establishment of non-native rainbow trout

Sofia Consuegra, Nia Phillips, Gonzalo Gajardo & Carlos Garcia De Leaniz
Aquaculture is a major source of invasive aquatic species, despite the fact that cultured organisms often have low genetic diversity and tend to be maladapted to survive in the wild. Yet, to what extent aquaculture escapees become established by means of high propagule pressure and multiple origins is not clear. We analysed the genetic diversity of 15 established populations and 4 farmed stocks of non-native rainbow trout in Chile, a species first introduced for recreational...

Data from: Nonadditive changes to cytosine methylation as a consequence of hybridization and genome duplication in Senecio (Asteraceae)

Matthew J Hegarty, Tom Batstone, Gary L Barker, Keith J Edwards, Richard J Abbott & Simon J Hiscock
The merger of two or more divergent genomes within an allopolyploid nucleus can facilitate speciation and adaptive evolution in flowering plants. Widespread changes to gene expression have been shown to result from interspecific hybridisation and polyploidy in a number of plant species, and attention has now shifted to determining the epigenetic processes which drive these changes. We present here an analysis of cytosine methylation patterns in triploid F1 Senecio (ragwort) hybrids and their allohexaploid derivatives....

Data from: An evolutionary modelling approach to understanding the factors behind plant invasiveness and community susceptibility to invasion

John Warren, Chris J Topping & Penri James
Ecologists have had limited success in understanding which introduced species may become invasive. An evolutionary model is used to investigate which traits are associated with invasiveness. Translocation experiments were simulated in which species were moved into similar but evolutionary younger communities. The main findings were that species that had previously been the most abundant in their original communities have significantly higher rates of establishment than did species that had previously occurred at low abundance in...

Data from: Best of both worlds? Association between outcrossing and parasite loads in a selfing fish

Amy Ellison, Joanne Cable & Sofia Consuegra
Mixed-mating strategies (i.e. intermediate levels of self-fertilization and outcrossing in hermaphrodites) are relatively common in plants and animals, but why self-fertilization (selfing) rates vary so much in nature has proved difficult to explain. We tested the hypothesis that parasites help maintain mixed-mating using a partially selfing fish (Kryptolebias marmoratus) as a model. We show that outcrossed progeny in the wild are genetically more diverse and less susceptible to multiple parasite infections than their selfed counterparts....

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