ORCID Profile
0000-0001-5392-8142
Current Organisation
The University of Edinburgh
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Publisher: Cold Spring Harbor Laboratory
Date: 14-09-2022
DOI: 10.1101/2022.09.12.507595
Abstract: Mutation, recombination, and transposition occurring during meiosis provide the variation on which natural selection can act and the rates at which they occur are important parameters in models of evolution. The de novo mutation rate determines levels of genetic ersity, responses to ongoing selection, and levels of genetic load. Recombination breaks up haplotypes and reduces the effects of linkage, helping to spread beneficial alleles and purge deleterious ones. Transposable elements (TE) selfishly replicate themselves through the genome, imposing fitness costs on the host and introducing complex mutations that can affect gene expression and give rise to new genes. However, even for key evolutionary models such as Drosophila melanogaster and D. simulans few estimates of these parameters are available, and we have little idea of how rates vary between in iduals, sexes, populations, or species. Here, we provide direct estimates of mutation, recombination, and transposition rates and their variation in a West African and a European population of D. melanogaster and a European population of D. simulans . Across 89 flies, we observe 58 single nucleotide mutations, 286 crossovers, and 89 TE insertions. Compared to the European D. melanogaster , we find the West African population has a lower mutation rate (1.67 vs . 4.86 × 10 −9 site −1 gen −1 ) and transposition rate (8.99 vs . 23.36 × 10 −5 copy −1 gen −1 ), but a higher recombination rate (3.44 vs . 2.06 cM/Mb). The European D. simulans population has a similar mutation rate to European D. melanogaster but a significantly higher recombination rate and a lower but not significantly different transposition rate. Overall, we find paternal-derived mutations are more frequent than maternal ones in both species. De novo mutation rates are 1.67 × 10 −9 site −1 gen −1 (95% HPD CI: 0.54 – 3.14 × 10 −9 ), 4.86 × 10 −9 site −1 gen −1 (2.11 – 8.02 × 10 −9 ), and 4.51 × 10 −9 site −1 gen −1 (1.94 – 7.75 × 10 −9 ) for the West African D. melanogaster , the European D. melanogaster and the European D. simulans population, respectively. In females, recombination rates in the absence of large genomic inversions are 3.44 cM/Mb (2.72 – 4.18), 2.06 cM/Mb (1.57 - 2.57), and 3.04 cM/Mb (2.45 - 3.73) for the three populations, respectively. There was no strong evidence of recombination observed in males. Mutations (SNMs and indels) are male-biased. The West African D. melanogaster population has a lower TE activity than the other populations and CMC-Transib is the dominant active TE. The European D. melanogaster population has multiple active TEs: Gypsy, CMC-Transib, Pao, Jockey and hAT-hobo while in European D. simulans , they are Gypsy, CMC-Transib, Pao, hAT-hobo, Copia and TcMar-Mariner .
Publisher: Cold Spring Harbor Laboratory
Date: 21-08-2019
DOI: 10.1101/741645
Abstract: Metagenomic sequencing has revolutionised our knowledge of virus ersity, with new virus sequences being reported faster than ever before. However, virus discovery from metagenomic sequencing usually depends on detectable homology: without a sufficiently close relative, so-called ‘dark’ virus sequences remain unrecognisable. An alternative approach is to use virus-identification methods that do not depend on detecting homology, such as virus recognition by host antiviral immunity. For ex le, virus-derived small RNAs have previously been used to propose ‘dark’ virus sequences associated with the Drosophilidae (Diptera). Here we combine published Drosophila data with a comprehensive search of transcriptomic sequences and selected meta-transcriptomic datasets to identify a completely new lineage of segmented positive-sense single-stranded RNA viruses that we provisionally refer to as the Quenyaviruses . Each of the five segments contains a single open reading frame, with most encoding proteins showing no detectable similarity to characterised viruses, and one sharing a small number of residues with the RNA-dependent RNA polymerases of single- and double-stranded RNA viruses. Using these sequences, we identify close relatives in approximately 20 arthropods, including insects, crustaceans, spiders and a myriapod. Using a more conserved sequence from the putative polymerase, we further identify relatives in meta-transcriptomic datasets from gut, gill, and lung tissues of vertebrates, reflecting infections of vertebrates or of their associated parasites. Our data illustrate the utility of small RNAs to detect viruses with limited sequence conservation, and provide robust evidence for a new deeply ergent and phylogenetically distinct RNA virus lineage.
Publisher: Oxford University Press (OUP)
Date: 22-07-2014
DOI: 10.1093/NAR/GKU657
Publisher: Oxford University Press (OUP)
Date: 2020
DOI: 10.1093/VE/VEZ061
Abstract: Metagenomic sequencing has revolutionised our knowledge of virus ersity, with new virus sequences being reported faster than ever before. However, virus discovery from metagenomic sequencing usually depends on detectable homology: without a sufficiently close relative, so-called ‘dark’ virus sequences remain unrecognisable. An alternative approach is to use virus-identification methods that do not depend on detecting homology, such as virus recognition by host antiviral immunity. For ex le, virus-derived small RNAs have previously been used to propose ‘dark’ virus sequences associated with the Drosophilidae (Diptera). Here, we combine published Drosophila data with a comprehensive search of transcriptomic sequences and selected meta-transcriptomic datasets to identify a completely new lineage of segmented positive-sense single-stranded RNA viruses that we provisionally refer to as the Quenyaviruses. Each of the five segments contains a single open reading frame, with most encoding proteins showing no detectable similarity to characterised viruses, and one sharing a small number of residues with the RNA-dependent RNA polymerases of single- and double-stranded RNA viruses. Using these sequences, we identify close relatives in approximately 20 arthropods, including insects, crustaceans, spiders, and a myriapod. Using a more conserved sequence from the putative polymerase, we further identify relatives in meta-transcriptomic datasets from gut, gill, and lung tissues of vertebrates, reflecting infections of vertebrates or of their associated parasites. Our data illustrate the utility of small RNAs to detect viruses with limited sequence conservation, and provide robust evidence for a new deeply ergent and phylogenetically distinct RNA virus lineage.
Publisher: Elsevier BV
Date: 07-2009
Publisher: Cold Spring Harbor Laboratory
Date: 25-01-2023
DOI: 10.1101/2023.01.24.525323
Abstract: Mutation is the ultimate source of all genetic variation, and over the last ten years the ready availability of whole-genome sequencing has permitted direct estimation of mutation rate for many non-model species across the tree of life. In this meta-analysis we make a comprehensive search of the literature for mutation rate estimates in eukaryotes, identifying 140 mutation accumulation (MA) and parent-offspring (PO) sequencing studies covering 134 species. Based on these data, we revisit differences in single nucleotide mutation (SNM) rate between different phylogenetic lineages and update the known relationships between mutation rate and generation time, genome size, and nucleotide ersity—while accounting for phylogenetic non-independence. We do not find a significant difference between MA and PO in estimated mutation rates, but we confirm that mammal and plant lineages have higher mutation rates than arthropods, and that unicellular eukaryotes have the lowest mutation rates. We find that mutation rates are higher in species with longer generation times and larger genome sizes, even when accounting for phylogenetic relationships. Moreover, although nucleotide ersity is positively correlated with mutation rate, the gradient of the relationship is significantly less than one (on a logarithmic scale), consistent with higher mutation rates in populations with smaller effective size. For the 29 species for which data are available, we find that indel mutation rates are positively correlated with nucleotide mutation rates, and that short deletions are generally more common than short insertions. Nevertheless, despite recent progress, no estimates of either SNM or indel mutation rates are available for the majority of deeply-branching eukaryotic lineages—or even for most animal phyla. Even among charismatic megafauna, experimental mutation rate estimates remain unknown for hibia and scarce for reptiles and fish. Over the past decade, the sequencing revolution has led to an ever-increasing number of mutation-rate estimates from mutation accumulation or parent-offspring sequencing studies in eukaryotes. However, studies rarely quantify to what extent the mutation rate varies among these species. Also, despite strong predictions as to how mutation rate should vary with (e.g.) generation time, there have been few recent or wide-ranging analyses of such predictors while accounting for the inherent similarity between closely-related species. Of particular note, there has been surprisingly little effort to robustly test the ‘drift barrier’ hypothesis that mutation rates should decrease with increasing effective population size. In this study, we used a comprehensive literature search to identify all the available experimental estimates of mutation rate in eukaryotes and subject them to phylogenetic mixed-model analyses. We find that per-nucleotide per-generation mutation rates differ by orders of magnitude among species: plants and mammals tend to have higher mutation rates than arthropods, and unicellular organisms have the lowest mutation rates. Our analysis also shows that mutation rates increase significantly with increasing generation time and genome size, and nucleotide ersity increases with mutation rate with a gradient less than one—as predicted by the drift-barrier hypothesis.
Publisher: Elsevier BV
Date: 08-2008
Location: United Kingdom of Great Britain and Northern Ireland
Location: United Kingdom of Great Britain and Northern Ireland
Location: United Kingdom of Great Britain and Northern Ireland
No related grants have been discovered for Darren Obbard.