List of works - Daniel Sloan

A recurring syndrome of accelerated plastid genome evolution in the angiosperm tribe Sileneae (Caryophyllaceae).

scientific article

An improved mitochondrial reference genome for Arabidopsis thaliana Col-0

Antisense transcription is pervasive but rarely conserved in enteric bacteria

scientific article published on 7 August 2012

Assessing mitochondrial function in angiosperms with highly divergent mitochondrial genomes

Assessing the fitness consequences of mitonuclear interactions in natural populations

scientific article published on 26 December 2018

Association Analysis Provides Insights into Plant Mitonuclear Interactions

scholarly article

Causes and consequences of rapidly evolving mtDNA in a plant lineage

scientific article published on 06 February 2017

Characterization of transcriptomes from sexual and asexual lineages of a New Zealand snail (Potamopyrgus antipodarum).

scientific article

Chromosome-Level Genome Assembly for the Angiosperm Silene conica

Combining tRNA sequencing methods to characterize plant tRNA expression and post-transcriptional modification

scientific article published on 25 July 2020

Complete Sequence of a 641-kb Insertion of Mitochondrial DNA in the Arabidopsis thaliana Nuclear Genome

scientific article published on 01 May 2022

Conservative and compensatory evolution in oxidative phosphorylation complexes of angiosperms with highly divergent rates of mitochondrial genome evolution

scientific article

Correction of Persistent Errors in Arabidopsis Reference Mitochondrial Genomes

scientific article published on 08 March 2018

Correlation between sequence divergence and polymorphism reveals similar evolutionary mechanisms acting across multiple timescales in a rapidly evolving plastid genome

scientific article

CyMIRA: The Cytonuclear Molecular Interactions Reference for Arabidopsis

scientific article published on 01 August 2019

Cytonuclear integration and co-evolution

scientific article published on 01 October 2018

Cytonuclear interactions and relaxed selection accelerate sequence evolution in organelle ribosomes

scientific article published on 13 December 2013

Cytonuclear responses to genome doubling

scientific article published on 01 September 2017

De novo transcriptome assembly and polymorphism detection in the flowering plant Silene vulgaris (Caryophyllaceae).

scientific article

Detecting Rare Mutations and DNA Damage with Sequencing-Based Methods.

scientific article

Disentangling associated genomes.

scientific article published in January 2013

Divergence-based introgression polarization

scientific article published on 27 March 2020

Do angiosperms with highly divergent mitochondrial genomes have altered mitochondrial function?

scientific article published on 21 June 2019

Endosymbiotic bacteria as a source of carotenoids in whiteflies

scientific article

Evolutionary feedbacks between reproductive mode and mutation rate exacerbate the paradox of sex.

scientific article

Evolutionary rate variation at multiple levels of biological organization in plant mitochondrial DNA

scientific article published on 01 December 2007

Extensive loss of RNA editing sites in rapidly evolving Silene mitochondrial genomes: selection vs. retroprocessing as the driving force

scientific article

Extensive loss of translational genes in the structurally dynamic mitochondrial genome of the angiosperm Silene latifolia.

scientific article

Extreme variation in rates of evolution in the plastid Clp protease complex

scientific article published on 28 January 2019

Gene content evolution in the arthropods

scientific article published on 23 January 2020

Gene duplication and rate variation in the evolution of plastid ACCase and Clp genes in angiosperms

scholarly article published in 2022

Gene-wise resampling outperforms site-wise resampling in phylogenetic coalescence analyses

article

Genome Reduction and Co-evolution between the Primary and Secondary Bacterial Symbionts of Psyllids ⬇️

scientific article (publication date: 10 August 2012)

Genome copy number predicts extreme evolutionary rate variation in plant mitochondrial DNA

High transcript abundance, RNA editing, and small RNAs in intergenic regions within the massive mitochondrial genome of the angiosperm Silene noctiflora

scientific article published on 14 November 2015

History of plastid DNA insertions reveals weak deletion and at mutation biases in angiosperm mitochondrial genomes.

scientific article

Homologous recombination changes the context of Cytochrome b transcription in the mitochondrial genome of Silene vulgaris KRA

Hopeful monsters: unintended sequencing of famously malformed mite mitochondrial tRNAs reveals widespread expression and processing of sense-antisense pairs

scientific article published on 12 January 2021

ILS-Aware Analysis of Low-Homoplasy Retroelement Insertions: Inference of Species Trees and Introgression Using Quartets

scientific article published on 01 April 2020

Interchangeable parts: The evolutionarily dynamic tRNA population in plant mitochondria

scientific article published on 14 March 2020

Intraspecific variation in mitochondrial genome sequence, structure, and gene content in Silene vulgaris, an angiosperm with pervasive cytoplasmic male sterility ⬇️

scientific article published on September 26, 2012

Linear Plasmids and the Rate of Sequence Evolution in Plant Mitochondrial Genomes.

scientific article

Little evidence for homoeologous gene conversion and homoeologous exchange events in Gossypium allopolyploids

Long-read transcriptome and other genomic resources for the angiosperm Silene noctiflora

scientific article published on 01 August 2021

MSH1 is required for maintenance of the low mutation rates in plant mitochondrial and plastid genomes

scientific article published on 29 June 2020

Mitochondrial Retroprocessing Promoted Functional Transfers of rpl5 to the Nucleus in Grasses

scientific article

Mitonuclear linkage disequilibrium in human populations

scientific article published in September 2015

Molecular Evolution: The Perplexing Diversity of Mitochondrial RNA Editing Systems

scientific article

Mutational pressure drives differential genome conservation in two bacterial endosymbionts of sap feeding insects

scientific article published on 04 December 2020

Non-coding RNA may be associated with cytoplasmic male sterility in Silene vulgaris

scientific article

Nuclear and mitochondrial RNA editing systems have opposite effects on protein diversity

scientific article published in August 2017

One ring to rule them all? Genome sequencing provides new insights into the 'master circle' model of plant mitochondrial DNA structure

scientific article published on December 2013

Parallel histories of horizontal gene transfer facilitated extreme reduction of endosymbiont genomes in sap-feeding insects

scientific article published on 06 January 2014

Partitioned coalescence support reveals biases in species-tree methods and detects gene trees that determine phylogenomic conflicts

scientific article published on 18 June 2019

Phylogenetic Relationships of Silene multinervia and Silene Section Conoimorpha (Caryophyllaceae)

scientific article published in 2012

Phylogenetic analysis of mitochondrial substitution rate variation in the angiosperm tribe Sileneae

scientific article

Phylogenetic analysis of mitochondrial substitution rate variation in the angiosperm tribe Sileneae

scholarly article by Daniel B Sloan et al published 2010 in BMC Evolutionary Biology

Plant functional types do not predict biomass responses to removal and fertilization in Alaskan tussock tundra

scientific article published on July 2008

Polyploid plants take cytonuclear perturbations in stride

Positive Selection in Rapidly Evolving Plastid-Nuclear Enzyme Complexes

scientific article

Rapid Shifts in Mitochondrial tRNA Import in a Plant Lineage with Extensive Mitochondrial tRNA Gene Loss

scientific article published on 01 December 2021

Rapid evolution of enormous, multichromosomal genomes in flowering plant mitochondria with exceptionally high mutation rates

scientific article

Recent acceleration of plastid sequence and structural evolution coincides with extreme mitochondrial divergence in the angiosperm genus Silene.

scientific article

Recombination and intraspecific polymorphism for the presence and absence of entire chromosomes in mitochondrial genomes

Selfish Mitonuclear Conflict

scientific article published on 01 June 2019

Sex, Mitochondria, and Genetic Rescue.

scientific article published on 19 December 2015

Stochastic organelle genome segregation through Arabidopsis development and reproduction

Termination of asymmetric cell division and differentiation of stomata

scientific article published on 20 December 2006

Testing for selection on synonymous sites in plant mitochondrial DNA: the role of codon bias and RNA editing

scientific article

The Draft Genome of Kochia scoparia and the Mechanism of Glyphosate Resistance via Transposon-Mediated EPSPS Tandem Gene Duplication

scientific article published on 01 October 2019

The Genomic Basis of Arthropod Diversity

article published in 2018

The Hologenome Concept: Helpful or Hollow?

scientific article published on 4 December 2015

The Mitonuclear Dimension of Neanderthal and Denisovan Ancestry in Modern Human Genomes.

scientific article published on June 2017

The Roles of Mutation, Selection, and Expression in Determining Relative Rates of Evolution in Mitochondrial versus Nuclear Genomes

scientific article published on 25 August 2016

The Tempo and Mode of Angiosperm Mitochondrial Genome Divergence Inferred from Intraspecific Variation in Arabidopsis thaliana

scientific article published on 05 March 2020

The decoupled evolution of the organellar genomes of Silene nutans leads to distinct roles in the speciation process

scientific article published in 2023

The effects of subsampling gene trees on coalescent methods applied to ancient divergences

scientific article

The evolution of genomic instability in the obligate endosymbionts of whiteflies

scientific article (publication date: 2013)

The massive mitochondrial genome of the angiosperm Silene noctiflora is evolving by gain or loss of entire chromosomes

scientific article

The mitochondrial genome of the legume Vigna radiata and the analysis of recombination across short mitochondrial repeats

scientific article

The on-again, off-again relationship between mitochondrial genomes and species boundaries

scientific article published on 20 December 2016

Using plants to elucidate the mechanisms of cytonuclear co-evolution

scientific article

Variation in mutation rate and polymorphism among mitochondrial genes of Silene vulgaris

scientific article

aPPRove: An HMM-Based Method for Accurate Prediction of RNA-Pentatricopeptide Repeat Protein Binding Events

scientific article

List of works by Daniel Sloan

A recurring syndrome of accelerated plastid genome evolution in the angiosperm tribe Sileneae (Caryophyllaceae).

An improved mitochondrial reference genome for Arabidopsis thaliana Col-0

Antisense transcription is pervasive but rarely conserved in enteric bacteria

Assessing mitochondrial function in angiosperms with highly divergent mitochondrial genomes

Assessing the fitness consequences of mitonuclear interactions in natural populations

Association Analysis Provides Insights into Plant Mitonuclear Interactions

Causes and consequences of rapidly evolving mtDNA in a plant lineage

Characterization of transcriptomes from sexual and asexual lineages of a New Zealand snail (Potamopyrgus antipodarum).

Chromosome-Level Genome Assembly for the Angiosperm <i>Silene conica</i>

Combining tRNA sequencing methods to characterize plant tRNA expression and post-transcriptional modification

Complete Sequence of a 641-kb Insertion of Mitochondrial DNA in the Arabidopsis thaliana Nuclear Genome

Conservative and compensatory evolution in oxidative phosphorylation complexes of angiosperms with highly divergent rates of mitochondrial genome evolution

Correction of Persistent Errors in Arabidopsis Reference Mitochondrial Genomes

Correlation between sequence divergence and polymorphism reveals similar evolutionary mechanisms acting across multiple timescales in a rapidly evolving plastid genome

CyMIRA: The Cytonuclear Molecular Interactions Reference for Arabidopsis

Cytonuclear integration and co-evolution

Cytonuclear interactions and relaxed selection accelerate sequence evolution in organelle ribosomes

Cytonuclear responses to genome doubling

De novo transcriptome assembly and polymorphism detection in the flowering plant Silene vulgaris (Caryophyllaceae).

Detecting Rare Mutations and DNA Damage with Sequencing-Based Methods.

Disentangling associated genomes.

Divergence-based introgression polarization

Do angiosperms with highly divergent mitochondrial genomes have altered mitochondrial function?

Endosymbiotic bacteria as a source of carotenoids in whiteflies

Evolutionary feedbacks between reproductive mode and mutation rate exacerbate the paradox of sex.

Evolutionary rate variation at multiple levels of biological organization in plant mitochondrial DNA

Extensive loss of RNA editing sites in rapidly evolving Silene mitochondrial genomes: selection vs. retroprocessing as the driving force

Extensive loss of translational genes in the structurally dynamic mitochondrial genome of the angiosperm Silene latifolia.

Extreme variation in rates of evolution in the plastid Clp protease complex

Extreme variation in rates of evolution in the plastid Clp protease complex

Gene content evolution in the arthropods

Gene duplication and rate variation in the evolution of plastid ACCase and Clp genes in angiosperms

Gene-wise resampling outperforms site-wise resampling in phylogenetic coalescence analyses

Genome Reduction and Co-evolution between the Primary and Secondary Bacterial Symbionts of Psyllids ⬇️

Genome copy number predicts extreme evolutionary rate variation in plant mitochondrial DNA

High transcript abundance, RNA editing, and small RNAs in intergenic regions within the massive mitochondrial genome of the angiosperm Silene noctiflora

History of plastid DNA insertions reveals weak deletion and at mutation biases in angiosperm mitochondrial genomes.

Homologous recombination changes the context of Cytochrome b transcription in the mitochondrial genome of Silene vulgaris KRA

Hopeful monsters: unintended sequencing of famously malformed mite mitochondrial tRNAs reveals widespread expression and processing of sense-antisense pairs

ILS-Aware Analysis of Low-Homoplasy Retroelement Insertions: Inference of Species Trees and Introgression Using Quartets

Interchangeable parts: The evolutionarily dynamic tRNA population in plant mitochondria

Intraspecific variation in mitochondrial genome sequence, structure, and gene content in Silene vulgaris, an angiosperm with pervasive cytoplasmic male sterility ⬇️

Linear Plasmids and the Rate of Sequence Evolution in Plant Mitochondrial Genomes.

Little evidence for homoeologous gene conversion and homoeologous exchange events in <i>Gossypium</i> allopolyploids

Long-read transcriptome and other genomic resources for the angiosperm Silene noctiflora

MSH1 is required for maintenance of the low mutation rates in plant mitochondrial and plastid genomes

Mitochondrial Retroprocessing Promoted Functional Transfers of rpl5 to the Nucleus in Grasses

Mitonuclear linkage disequilibrium in human populations

Molecular Evolution: The Perplexing Diversity of Mitochondrial RNA Editing Systems

Mutational pressure drives differential genome conservation in two bacterial endosymbionts of sap feeding insects

Non-coding RNA may be associated with cytoplasmic male sterility in Silene vulgaris

Nuclear and mitochondrial RNA editing systems have opposite effects on protein diversity

One ring to rule them all? Genome sequencing provides new insights into the 'master circle' model of plant mitochondrial DNA structure

Parallel histories of horizontal gene transfer facilitated extreme reduction of endosymbiont genomes in sap-feeding insects

Partitioned coalescence support reveals biases in species-tree methods and detects gene trees that determine phylogenomic conflicts

Phylogenetic Relationships of Silene multinervia and Silene Section Conoimorpha (Caryophyllaceae)

Phylogenetic analysis of mitochondrial substitution rate variation in the angiosperm tribe Sileneae

Phylogenetic analysis of mitochondrial substitution rate variation in the angiosperm tribe Sileneae

Plant functional types do not predict biomass responses to removal and fertilization in Alaskan tussock tundra

Polyploid plants take cytonuclear perturbations in stride

Positive Selection in Rapidly Evolving Plastid-Nuclear Enzyme Complexes

Rapid Shifts in Mitochondrial tRNA Import in a Plant Lineage with Extensive Mitochondrial tRNA Gene Loss

Rapid evolution of enormous, multichromosomal genomes in flowering plant mitochondria with exceptionally high mutation rates

Recent acceleration of plastid sequence and structural evolution coincides with extreme mitochondrial divergence in the angiosperm genus Silene.

Recombination and intraspecific polymorphism for the presence and absence of entire chromosomes in mitochondrial genomes

Selfish Mitonuclear Conflict

Sex, Mitochondria, and Genetic Rescue.

Stochastic organelle genome segregation through <i>Arabidopsis</i> development and reproduction

Termination of asymmetric cell division and differentiation of stomata

Testing for selection on synonymous sites in plant mitochondrial DNA: the role of codon bias and RNA editing

The Draft Genome of Kochia scoparia and the Mechanism of Glyphosate Resistance via Transposon-Mediated EPSPS Tandem Gene Duplication

The Genomic Basis of Arthropod Diversity

The Hologenome Concept: Helpful or Hollow?

The Mitonuclear Dimension of Neanderthal and Denisovan Ancestry in Modern Human Genomes.

The Roles of Mutation, Selection, and Expression in Determining Relative Rates of Evolution in Mitochondrial versus Nuclear Genomes

The Tempo and Mode of Angiosperm Mitochondrial Genome Divergence Inferred from Intraspecific Variation in Arabidopsis thaliana

The decoupled evolution of the organellar genomes of <i>Silene nutans</i> leads to distinct roles in the speciation process

The effects of subsampling gene trees on coalescent methods applied to ancient divergences

The evolution of genomic instability in the obligate endosymbionts of whiteflies