25 Works

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: 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...

Additional file 2 of LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis

Ezgi Özkurt, Joachim Fritscher, Nicola Soranzo, Duncan Y. K. Ng, Robert P. Davey, Mohammad Bahram & Falk Hildebrand
Additional file 2: Supplementary Table S2. Significance of differences between each pipeline in the reproducibility of beta diversity between the technical replicates. Significance of differences in Bray-Curtis distance between the pipelines were calculated based on the Tukey’s HSD test.

Additional file 2 of Crop management shapes the diversity and activity of DNA and RNA viruses in the rhizosphere

George Muscatt, Sally Hilton, Sebastien Raguideau, Graham Teakle, Ian D. E. A. Lidbury, Elizabeth M. H. Wellington, Christopher Quince, Andrew Millard, Gary D. Bending & Eleanor Jameson
Additional file 2: Supplementary Table S1. Sample metadata for all sample libraries. Supplementary Table S2. DNA viral population read counts. Supplementary Table S3. ssRNA viral population read counts. Supplementary Table S4. 16S rRNA OTU read counts. Supplementary Table S5. Viral gene read counts. Supplementary Table S6. PERMANOVA testing of contribution of soil compartment, crop rotation strategy and growth stage on viral and bacterial community composition. Supplementary Table S7. Mixed effect model output for linear relationship...

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...

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...

Additional file 1 of LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis

Ezgi Özkurt, Joachim Fritscher, Nicola Soranzo, Duncan Y. K. Ng, Robert P. Davey, Mohammad Bahram & Falk Hildebrand
Additional file 1: Supplementary Table S1. Read counts and number of OTUs/ASVs in the OTU/ASV matrix of each pipeline.

Additional file 4 of LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis

Ezgi Özkurt, Joachim Fritscher, Nicola Soranzo, Duncan Y. K. Ng, Robert P. Davey, Mohammad Bahram & Falk Hildebrand
Additional file 4: Supplementary Table S4. Accuracy of each pipeline in re-constructing the mock community at genus level.

First large-scale quantification study of DNA preservation in insects from natural history collections using genome-wide sequencing

Victoria Elizabeth Mullin, William Stephen, Andres Arce, Will Nash, Calum Raine, David Notton, Ashleigh Whiffin, Vladimir Blagoderov, Karim Gharbi, James Hogan, Tony Hunter, Naomi Irish, Simon Jackson, Steve Judd, Chris Watkins, Wilfried Haerty, Jeff Ollerton, Selina Brace, Richard Gill & Ian Barnes
Insect declines are a global issue with significant ecological and economic ramifications. Yet we have a poor understanding of the genomic impact these losses can have. Genome-wide data from historical specimens has the potential to provide baselines of population genetic measures to study population change, with natural history collections representing large repositories of such specimens. However, an initial challenge in conducting historical DNA data analyses, is to understand how molecular preservation varies between specimens. Here,...

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.

Additional file 1 of LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis

Ezgi Özkurt, Joachim Fritscher, Nicola Soranzo, Duncan Y. K. Ng, Robert P. Davey, Mohammad Bahram & Falk Hildebrand
Additional file 1: Supplementary Table S1. Read counts and number of OTUs/ASVs in the OTU/ASV matrix of each pipeline.

Additional file 5 of LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis

Ezgi Özkurt, Joachim Fritscher, Nicola Soranzo, Duncan Y. K. Ng, Robert P. Davey, Mohammad Bahram & Falk Hildebrand
Additional file 5: Supplementary Figure S1. Galaxy web interface of LotuS2. Raw reads can be uploaded into the LotuS2 via the Galaxy web interface and analysed (accessible on https://usegalaxy.eu/ ).

Additional file 2 of Crop management shapes the diversity and activity of DNA and RNA viruses in the rhizosphere

George Muscatt, Sally Hilton, Sebastien Raguideau, Graham Teakle, Ian D. E. A. Lidbury, Elizabeth M. H. Wellington, Christopher Quince, Andrew Millard, Gary D. Bending & Eleanor Jameson
Additional file 2: Supplementary Table S1. Sample metadata for all sample libraries. Supplementary Table S2. DNA viral population read counts. Supplementary Table S3. ssRNA viral population read counts. Supplementary Table S4. 16S rRNA OTU read counts. Supplementary Table S5. Viral gene read counts. Supplementary Table S6. PERMANOVA testing of contribution of soil compartment, crop rotation strategy and growth stage on viral and bacterial community composition. Supplementary Table S7. Mixed effect model output for linear relationship...

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...

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

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...

Whole genome resequencing data enables a targeted SNP panel for conservation and aquaculture of Oreochromis cichlid fishes

Adam Ciezarek, Antonia Ford, Graham Etherington, Nasser Kasozi, Milan Malinsky, Tarang Mehta, Luca Penso-Dolfin, Benjamin Ngatunga, Asilatu Shechonge, Rashid Tamatamah, Wilfried Haerty, Federica Di Palma, Martin Genner & Turner George
Cichlid fish of the genus Oreochromis form the basis of the global tilapia aquaculture and fisheries industries. Broodstocks for aquaculture are often collected from wild populations, which in Africa may be from locations containing multiple Oreochromis species. However, many species are difficult to distinguish morphologically, hampering efforts to maintain good quality farmed strains. Additionally, non-native farmed tilapia populations are known to be widely distributed across Africa and to hybridize with native Oreochromis species, which themselves...

Additional file 4 of LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis

Ezgi Özkurt, Joachim Fritscher, Nicola Soranzo, Duncan Y. K. Ng, Robert P. Davey, Mohammad Bahram & Falk Hildebrand
Additional file 4: Supplementary Table S4. Accuracy of each pipeline in re-constructing the mock community at genus level.

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: 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 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...

Additional file 3 of LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis

Ezgi Özkurt, Joachim Fritscher, Nicola Soranzo, Duncan Y. K. Ng, Robert P. Davey, Mohammad Bahram & Falk Hildebrand
Additional file 3: Supplementary Table S3. Correlation and beta distance between the mock community and re-constructed mock community by each pipeline. A-B) Spearman and Pearson correlation between the expected abundances in the mock community and the observed abundances by each pipeline. C) Bray-Curtis dissimilarity between the known mock community and re-constructed mock community composition by each pipeline.

Additional file 2 of LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis

Ezgi Özkurt, Joachim Fritscher, Nicola Soranzo, Duncan Y. K. Ng, Robert P. Davey, Mohammad Bahram & Falk Hildebrand
Additional file 2: Supplementary Table S2. Significance of differences between each pipeline in the reproducibility of beta diversity between the technical replicates. Significance of differences in Bray-Curtis distance between the pipelines were calculated based on the Tukey’s HSD test.

Additional file 3 of LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis

Ezgi Özkurt, Joachim Fritscher, Nicola Soranzo, Duncan Y. K. Ng, Robert P. Davey, Mohammad Bahram & Falk Hildebrand
Additional file 3: Supplementary Table S3. Correlation and beta distance between the mock community and re-constructed mock community by each pipeline. A-B) Spearman and Pearson correlation between the expected abundances in the mock community and the observed abundances by each pipeline. C) Bray-Curtis dissimilarity between the known mock community and re-constructed mock community composition by each pipeline.

Additional file 5 of LotuS2: an ultrafast and highly accurate tool for amplicon sequencing analysis

Ezgi Özkurt, Joachim Fritscher, Nicola Soranzo, Duncan Y. K. Ng, Robert P. Davey, Mohammad Bahram & Falk Hildebrand
Additional file 5: Supplementary Figure S1. Galaxy web interface of LotuS2. Raw reads can be uploaded into the LotuS2 via the Galaxy web interface and analysed (accessible on https://usegalaxy.eu/ ).

Registration Year

  • 2022
    13
  • 2021
    2
  • 2020
    2
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    1
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Resource Types

  • Dataset
    25

Affiliations

  • Earlham Institute
    25
  • Swedish University of Agricultural Sciences
    10
  • University of Tartu
    10
  • Quadram Institute
    10
  • University of East Anglia
    7
  • Bangor University
    4
  • University of Sheffield
    4
  • University of Leicester
    3
  • Tanzania Fisheries Research Institute
    2
  • University of Warwick
    2