11 Works

Data from: PyroClean: Denoising pyrosequences from protein-coding amplicons for the recovery of interspecific and intraspecific genetic variation

Ricardo Ramirez-Gonzalez, Douglas W. Yu, Catharine Bruce, Darren Heavens, Mario Caccamo & Brent C. Emerson
DatasetsThis .zip files contains two folders. The folder "Control" contains the 15 raw 454 sequence files generated from the "Test Pools" analysis detailed in Table 2 of the manuscript, and a file of 27 Sanger sequences listed in Table S1. The folder "Tenerife" contains the 6 raw 454 sequence files associated generated from the "Tenerife Forest Samples" analysis detailed in Table 3 of the manuscript.

Nucleotide alignments of eight meiosis genes under extreme selection following whole genome duplication in Arabidopsis lyrata/A.arenosa.

Paul Seear, Martin France, Catherine Gregory, Darren Heavens, Roswitha Schmickl, Levi Yant & James Higgins
In this study we performed a genotype-phenotype association analysis of meiotic stability in ten autotetraploid Arabidopsis lyrata and A. lyrata/A. arenosa hybrid populations collected from the Wachau region and East Austrian Forealps. The aim was to determine the effect of eight meiosis genes under extreme selection upon adaptation to whole genome duplication. Individual plants were genotyped by high-throughput sequencing of the eight meiosis genes (ASY1, ASY3, PDS5b, PRD3, REC8, SMC3, ZYP1a/b) implicated in synaptonemal complex...

Newly discovered cichlid fish biodiversity threatened by hybridization with non-native species - Data supporting published version

Martin Genner, Tabitha Blackwell, Antonia Ford, Adam Ciezarek, Stephanie Bradbeer, Carlos Gracida-Juarez, Alan Smith, Benjamin Ngatunga, Asilatu Shechonge, Rashid Tamatamah, Graham Etherington, Wilfried Haerty, Federica Di Palma & George Turner
Invasive freshwater fish systems are known to readily hybridize with indigenous congeneric species, driving loss of unique and irreplaceable genetic resources. Here we reveal that newly discovered (2013-2016) evolutionarily significant populations of Korogwe tilapia (Oreochromis korogwe) from southern Tanzania are threatened by hybridization with the larger invasive Nile tilapia (Oreochromis niloticus). We use a combination of morphology, microsatellite allele frequencies and whole genome sequences to show that O. korogwe from southern lakes (Nambawala, Rutamba and...

Data from: Contribution of maternal effects to dietary selection in Mediterranean fruit flies.

Philip T. Leftwich, William J. Nash, Lucy A. Friend & Tracey Chapman
Individual responses to dietary variation represent a fundamental component of fitness, and nutritional adaptation can occur over just a few generations. Maternal effects can show marked proximate responses to nutrition, but whether they contribute to longer-term dietary adaptation is unclear. Here we tested the hypotheses that maternal effects: (i) contribute to dietary adaptation, (ii) diminish when dietary conditions are constant between generations, (iii) are trait-specific and (iv) interact with high- and low-quality food. We used...

Data from: Adaptive phenotypic response to climate enabled by epigenetics in a K-strategy species, the fish Leucoraja ocellata (Rajidae)

Jackie Lighten, Danny Incarnato, Ben J. Ward, Cock Van Oosterhout, Ian Bradbury, Mark Hanson & Paul Bentzen
The relative importance of genetic versus epigenetic changes in adaptive evolution is a hotly debated topic, with studies showing that some species appear to be able to adapt rapidly without significant genetic change. Epigenetic mechanisms may be particularly important for the evolutionary potential of species with long maturation times and low reproductive potential (‘K-strategists’), particularly when faced with rapidly changing environmental conditions. Here we study the transcriptome of two populations of the winter skate (Leucoraja...

Data from: Genomic associations with bill length and disease reveal drift and selection across island bird populations

Claire Armstrong, David S. Richardson, Helen Hipperson, Gavin J. Horsburgh, Clemens Kuepper, Lawrence Percival-Alwyn, Matt Clark, Terry Burke & Lewis G. Spurgin
Island species provide excellent models for investigating how selection and drift operate in wild populations, and for determining how these processes act to influence local adaptation and speciation. Here, we examine the role of selection and drift in shaping genomic and phenotypic variation across recently separated populations of Berthelot's pipit (Anthus berthelotii), a passerine bird endemic to three archipelagos in the Atlantic. We first characterised genetic diversity and population structuring, which supported previous inferences of...

No severe genetic bottleneck in a rapidly range-expanding bumblebee pollinator

Ryan Edward Brock, Liam Crowther, David Wright, David Richardson, Claire Carvell, Martin Taylor & Andrew Bourke
Genetic bottlenecking can limit the success of populations colonising new ranges. However, successful colonisations can occur despite bottlenecking, a phenomenon known as the genetic paradox of invasion. Eusocial Hymenoptera such as bumblebees (Bombus spp.) should be particularly vulnerable to genetic bottlenecking, since homozygosity at the sex-determining locus leads to costly diploid male production. The Tree Bumblebee (B. hypnorum) has rapidly colonised the UK since 2001 and has been highlighted as exemplifying the genetic paradox of...

Data from: Inter- and intra-specific genomic divergence in Drosophila montana shows evidence for cold adaptation

Darren J. Parker, R. Axel W. Wiberg, Urmi Trivedi, Venera I. Tyukmaeva, Karim Gharbi, Roger K. Butlin, Anneli Hoikkala, Maaria Kankare & Michael G. Ritchie
D. montana gff fileGenome annotation file for D. montana genome (Accession number: LUVX00000000)D.mont_freeze_v1.4.gff.txt

Data from: Genome-guided investigation of plant natural product biosynthesis

Franziska Kellner, Jeongwoon Kim, Bernardo J. Clavijo, John P. Hamilton, Kevin L. Childs, Brieanne Vaillancourt, Jason Cepela, Marc Habermann, Burkhard Steuernagel, Leah Clissold, Kirsten McLay, Carol Robin Buell & Sarah E. O'Connor
The medicinal plant Madagascar periwinkle, Catharanthus roseus (L.) G. Don, produces hundreds of biologically active monoterpene-derived indole alkaloid (MIA) metabolites and is the sole source of the potent, expensive anti-cancer compounds vinblastine and vincristine. Access to a genome sequence would enable insights into the biochemistry, control, and evolution of genes responsible for MIA biosynthesis. However, generation of a near-complete, scaffolded genome is prohibitive to small research communities due to the expense, time, and expertise required....

Data from: The effects of recombination, mutation and selection on the evolution of the Rp1 resistance genes in grasses

Agathe Jouet, Mark McMullan & Cock Van Oosterhout
Plant immune genes, or resistance genes, are involved in a co-evolutionary arms race with a diverse range of pathogens. In agronomically important grasses, such R genes have been extensively studied because of their role in pathogen resistance and in the breeding of resistant cultivars. In this study, we evaluate the importance of recombination, mutation and selection on the evolution of the R gene complex Rp1 of Sorghum, Triticum, Brachypodium, Oryza and Zea. Analyses show that...

Data from: The laboratory domestication of zebrafish: from diverse populations to inbred substrains

Jaanus Suurväli, Andrew R. Whiteley, Yichen Zheng, Karim Gharbi, Maria Leptin & Thomas Wiehe
We know from human genetic studies that practically all aspects of biology are strongly influenced by the genetic background, as reflected in the advent of ‘personalized medicine’. Yet, with few exceptions, this is not taken into account when using laboratory populations as animal model systems for research in these fields. Laboratory strains of zebrafish (Danio rerio) are widely used for research in vertebrate developmental biology, behaviour and physiology, for modelling diseases, and for testing pharmaceutic...

Registration Year

  • 2021
    1
  • 2020
    2
  • 2019
    1
  • 2018
    3
  • 2016
    1
  • 2015
    2
  • 2013
    1

Resource Types

  • Dataset
    11

Affiliations

  • Earlham Institute
    11
  • University of East Anglia
    6
  • University of Sheffield
    2
  • Max Planck Institute for Ornithology
    1
  • Bangor University
    1
  • University of Montana
    1
  • Tanzania Fisheries Research Institute
    1
  • Centre for Ecology and Hydrology
    1
  • University of Cologne
    1
  • University of Lausanne
    1