Publications
2024
Sloan DB, Broz AK, Kuster SA, Muthye V, Peñafiel-Ayala A, Marron JR, Lavrov DV, Brieba LG. Submitted. Expansion of the MutS gene family in plants. bioRxiv pre-print
Waneka G, Broz AK, Wold-McGimsey F, Zou Y, Wu Z, Sloan DB. Submitted. Disruption of recombination machinery alters the mutational landscape in plant organellar genomes. bioRxiv pre-print
Waneka G, Pate B, Monroe JG, Sloan DB. Submitted. Investigating low frequency somatic mutations in Arabidopsis with Duplex Sequencing. bioRxiv pre-print
Moraga C et al. [52 co-authors, including Sloan DB]. Submitted. The Silene latifolia genome and its giant Y chromosome. bioRxiv pre-print
DeTar RA, Chustecki J, Martinez-Hottovy A, Cerrioti LF, Broz AK, Sanchez-Puerta MV, Elowsky C, Christensen AC, Sloan DB. Submitted. Photosynthesis drives retention of bacterial-like tRNA metabolism in plant organelles. bioRxiv pre-print
Conover JL, Grover CE, Sharbrough J, Sloan DB, Peterson DG, Wendel JF. In Press. Little evidence for homoeologous gene conversion and homoeologous exchange events in Gossypium allopolyploids. American Journal of Botany. bioRxiv pre-print
Waneka G, Stewart J, Anderson JR, Li W, Wilusz J, Argueso JL, Sloan DB. 2024. UV damage induces production of mitochondrial DNA fragments with specific length profiles. Genetics. 227: iyae070.
Peñafiel-Ayala A, Peralta-Castro A, Mora-Garduño J, García-Medel P, Zambrano-Pereira A, Díaz-Quezada C, Sloan DB, Brieba LG. 2024. Plant organellar MSH1 is a displacement loop specific endonuclease. Plant Cell and Physiology. 65: 560-575.
Sloan DB, Conover JL, Grover CE, Wendel JF, Sharbrough J. 2024. Polyploid plants take cytonuclear perturbations in stride. Plant Cell. 36: 829-839.
Zwonitzer K, Tressel L, Wu Z, Kan S, Broz AK, Mower JP, Ruhlman TA, Jansen RK, Sloan DB, Havird JC. 2024. Genome copy number predicts extreme evolutionary rate variation in plant mitochondrial DNA. Proceedings of the National Academy of Sciences. 121: e2317240121.
Lian Q, Li S, Kan K, Liao X, Huang S, Sloan DB, Wu Z. 2024. Association analysis provides insights into plant mitonuclear interactions. Molecular Biology and Evolution. 41: msae028.
Broz AK, Sloan DB, Johnston IG. 2024. Dynamics of organelle DNA segregation in Arabidopsis development and reproduction revealed with tissue-specific heteroplasmy profiling and stochastic modelling. New Phytologist. 241: 896-910.
2023
Fields PD, Weber MM, Waneka G, Broz AK, Sloan DB. 2023. Chromosome-level genome assembly for the angiosperm Silene conica. Genome Biology and Evolution. 15: evad192.
Warren JM, Broz, AK, Martinez-Hottovy A, Elowsky C, Christensen AC, Sloan DB. 2023. Rewiring of aminoacyl-tRNA synthetase localization and interactions in plants with extensive mitochondrial tRNA gene loss. Molecular Biology and Evolution. 40: msad163.
Postel Z, Sloan, DB, Gallina, S, Godé C, Schmitt, E, Mangenot, S, Drouard, L, Varré, J-S; Touzet, P. 2023. The decoupled evolution of the organellar genomes of Silene nutans leads to distinct roles in the speciation process. New Phytologist. 239: 766-777.
Giannakis K, Broz AK, Sloan DB, Johnston IG. 2023. Avoiding misleading estimates using mtDNA heteroplasmy statistics to study bottleneck size and selection. G3: Genes I Genomes I Genetics. 13: jkad068.
Sloan DB, DeTar RA, Warren JM. 2023. Aminoacyl-tRNA synthetase evolution within the dynamic tripartite translation system of plant cells. Genome Biology and Evolution. 15: evad050.
Sloan DB, Warren JM, Williams AM, Kuster SA, Forsythe ES. 2023. Incompatibility and interchangeability in molecular evolution. Genome Biology and Evolution. 15: evac184.
2022
Zou Y, Zhu W, Sloan DB, Wu Z. 2022. Long-read sequencing characterizes mitochondrial and plastid genome variants in Arabidopsis msh1 mutants. Plant Journal. 112: 738-755.
Grover CE, Forsythe ES, Sharbrough J, Miller ER, Conover JL, DeTar RA, Chavarro CF, Arick MA, Peterson DG, Leal-Bertioli SCM, Sloan DB, Wendel JF. 2022. Variation in cytonuclear expression accommodation among allopolyploid plants. Genetics. 222: iyac118.
Broz AK, Keene A, Fernandes Gyorfy M, Hodous M, Johnston IG, Sloan DB. 2022. Sorting of mitochondrial and plastid heteroplasmy in Arabidopsis is extremely rapid and depends on MSH1 activity. Proceedings of the National Academy of Sciences. 119: e2206973119.
Forsythe ES, Grover CE, Miller ER, Conover JL, Chavarro CF, Arick MA, Peterson DG, Leal-Bertioli SCM, Sharbrough J, Wendel JF, Sloan DB. 2022. Organellar transcripts dominate the cellular mRNA pool across plants of varying ploidy levels. Proceedings of the National Academy of Sciences. 119: e2204187119.
Fields PD, Waneka G, Naish M, Schatz MC, Henderson IR, Sloan DB. 2022. Complete sequence of a 641-kb insertion of mitochondrial DNA in the Arabidopsis thaliana nuclear genome. Genome Biology and Evolution. 14: evac059.
Sharbrough J, Conover JL, Fernandes Gyorfy M, Grover CE, Miller ER, Wendel JF, Sloan DB. 2022. Global patterns of subgenome evolution in organelle-targeted genes of six allotetraploid angiosperms. Molecular Biology and Evolution. 39: msac074.
Rei Liao JY; Friso G; Forsythe ES; Williams AM; Michel EJS; Buraraev SS; Ponnala L; Sloan DB, van Wijk KJ. 2022. Proteomics, phylogenetics, and co-expression analyses indicate novel interactions in the plastid CLP chaperone-protease system. Journal of Biological Chemistry. 298: 101609
Abdel-Ghany SE, LaManna LM, Harroun HT, Maliga P, Sloan DB. 2022. Rapid sequence evolution is associated with genetic incompatibilities in the plastid Clp complex. Plant Molecular Biology. 108: 277-287.
Williams AM, Carter OG, Forsythe ES, Mendoza HK, Sloan DB. 2022. Gene duplication and rate variation in the evolution of plastid ACCase and Clp genes in angiosperms. Molecular Phylogenetics and Evolution. 168: 107395.
Gatesy J, Sloan DB, Warren JM, Simmons MP, Springer MS. 2022. Iterative deletion of gene trees detects extreme biases in distance-based phylogenomic coalescent analyses. bioRxiv. 2022.03.08.483551. [pre-print only]
2021
Warren JM, Salinas-Giegé T, Triant DA, Taylor DR, Drouard L, Sloan DB. 2021. Rapid shifts in mitochondrial tRNA import in a plant lineage with extensive mitochondrial tRNA gene loss. Molecular Biology and Evolution. 38: 5735-5751.
Fernandes Gyorfy M, Miller ER, Conover JL, Grover CE, Wendel JF, Sloan DB, Sharbrough J. 2021. Nuclear-cytoplasmic balance: whole genome duplications induce elevated organellar genome copy number. Plant Journal. 108: 219–230.
Waneka G, Svendsen JM, Havird JC, Sloan DB. 2021. Mitochondrial mutations in Caenorhabditis elegans show signatures of oxidative damage and an AT-bias. Genetics. 219: iyab116.
Williams AM, Itgen MW, Broz AK, Carter OG, Sloan DB. 2021. Long-read transcriptome and other genomic resources for the angiosperm Silene noctiflora. G3: Genes I Genomes I Genetics. 11: jkab189.
Forsythe ES, William AM, Sloan DB. 2021. Genome-wide signatures of plastid-nuclear coevolution point to repeated perturbations of plastid proteostasis systems across angiosperms. Plant Cell. 33: 980-997.
Broz AK, Waneka G, Wu Z, Fernandes Gyorfy M, Sloan DB. 2021. Detecting de novo mitochondrial mutations in angiosperms with highly divergent evolutionary rates. Genetics. 218: iyab039.
Warren JM, Sloan DB. 2021. Hopeful monsters: Unintended sequencing of famously malformed mite mitochondrial tRNAs reveals widespread expression and processing of sense-antisense pairs. NAR Genomics and Bioinformatics. 3: lqaa111.
Waneka G, Vasquez YM, Bennett GM, Sloan DB. 2021. Mutational pressure drives differential genome conservation in two bacterial endosymbionts of sap-feeding insects. Genome Biology and Evolution. 13: evaa254.
Warren JM, Salinas-Giegé T, Hummel G, Coots NL, Svendsen JM, Brown KC, Drouard L, Sloan DB. 2021. Combining tRNA sequencing methods to characterize plant tRNA expression and post-transcriptional modification. RNA Biology. 18: 64-78.
2020
Wu Z, Waneka G, Broz AK, King CR, Sloan DB. 2020. MSH1 is required for maintenance of the low mutation rates in plant mitochondrial and plastid genomes. Proceedings of the National Academy of Sciences. 117: 16448-16455.
Forsythe ES, Sloan DB, Beilstein MA. 2020. Divergence-based introgression polarization. Genome Biology and Evolution. 12: 463-478.
Springer MS, Molloy EK, Sloan DB, Simmons MP, Gatesy J. 2020. ILS-aware analysis of low-homoplasy retroelement insertions: Inference of species trees and introgression using quartets. Journal of Heredity. 111: 147-168.
Warren JM, Sloan DB. 2020. Interchangeable parts: The evolutionarily dynamic tRNA population in plant mitochondria. Mitochondrion. 52: 144-156.
Wu Z, Waneka G, Sloan DB. 2020. The tempo and mode of angiosperm mitochondrial genome divergence inferred from intraspecific variation in Arabidopsis thaliana. G3: Genes I Genomes I Genetics. 10: 1077-1086.
Thomas GWC et al. [79 co-authors, including Sloan DB]. 2020. Gene content evolution in the arthropods. Genome Biology. 21:15.
2019
Patterson EL, Saski CA, Sloan DB, Tranel PJ, Westra P, Gaines TA. 2019. The draft genome of Kochia scoparia and the mechanism of glyphosate resistance via transposon-mediated EPSPS tandem gene duplication. Genome Biology and Evolution. 11: 2927-2940.
Forsythe ES, Sharbrough J, Havird JC, Warren JM, Sloan DB. 2019. CyMIRA: The Cytonuclear Molecular Interactions Reference for Arabidopsis. Genome Biology and Evolution. 11: 2194–2202.
Gatesy J, Sloan DB, Warren JM, Baker RH, Simmons MP, Springer MS. 2019. Partitioned coalescence support reveals biases in species-tree methods and pinpoints gene trees that determine phylogenomic conflicts. Molecular Phylogenetics and Evolution. 139: 106539.
Havird JC, Noe GR, Link L, Torres A, Logan DC, Sloan DB, Chicco AJ. 2019. Do angiosperms with highly divergent mitochondrial genomes have altered mitochondrial function? Mitochondrion. 49: 1-11.
Havird JC, Forsythe ES, Williams AM, Werren JH, Dowling DK, Sloan DB. 2019. Selfish mitonuclear conflict. Current Biology. 29: R496–R511.
Hill GE, Havird JC, Sloan DB, Burton RS, Greening C, Dowling DK. 2019. Assessing the fitness consequences of mitonuclear interactions in natural populations. Biological Reviews. 94: 1089-1104.
Wu Z, Sloan DB. 2019. Recombination and intraspecific polymorphism for the presence and absence of entire chromosomes in mitochondrial genomes. Heredity. 122: 647-659.
Williams AM, Friso G, van Wijk KJ, Sloan DB. 2019. Extreme variation in rates of evolution in the plastid Clp protease complex. Plant Journal. 98: 243-259.
Simmons MP, Sloan DB, Springer MS, Gatesy J. 2019. Gene-wise resampling outperforms site-wise resampling in phylogenetic coalescence analyses. Molecular Phylogenetics and Evolution. 131: 80-92.
2018
Štorchová H, Stone JD, Sloan DB, Abeyawardana O, Müller K, Walterová J, Pažoutová M. 2018. Homologous recombination changes the context of Cytochrome b transcription in the mitochondrial genome of Silene vulgaris KRA. BMC Genomics. 19: 874.
Sloan DB, Warren JM, Williams AW, Wu Z, Abdel-Ghany SE, Chicco AJ, Havird JC. 2018. Cytonuclear integration and co-evolution. Nature Reviews Genetics. 19: 635-648.
Sloan DB, Broz AK, Sharbrough J, Wu Z. 2018. Detecting rare mutations and DNA damage with sequencing-based methods. Trends in Biotechnology. 36: 729-740.
Sloan DB, Wu Z, Sharbrough J. 2018. Correction of persistent errors in Arabidopsis reference mitochondrial genomes. Plant Cell. 30: 525-527.
2017
Sharbrough J, Conover JL, Tate JA, Wendel JF, Sloan DB. 2017. Cytonuclear responses to genome doubling. American Journal of Botany. 104: 1277-1280.
Sloan DB. 2017. Nuclear and mitochondrial RNA editing systems have opposite effects on protein diversity. Biology Letters. 13:20170314.
Wu Z, Sloan DB, Brown CW, Rosenblueth M, Palmer JD, Ong HC. 2017. Mitochondrial retroprocessing promoted functional transfers of rpl5 to the nucleus in grasses. Molecular Biology and Evolution. 34:2340-2354.
Sharbrough J, Havird JC, Noe GR, Warren JM, Sloan DB. 2017. The mitonuclear dimension of Neanderthal and Denisovan ancestry in modern human genomes. Genome Biology and Evolution. 9:1567-1581.
Stone JD, Koloušková P, Sloan DB, Štorchová H. 2017. Non-coding RNA may be associated with cytoplasmic male sterility in Silene vulgaris. Journal of Experimental Botany. 68: 1599-1612.
Havird JC, Trapp P, Miller C, Bazos I, Sloan DB. 2017. Causes and consequences of rapidly evolving mtDNA in a plant lineage. Genome Biology and Evolution. 9: 323-336.
Sloan DB, Havird JC, Sharbrough J. 2017. The on-again, off-again relationship between mitochondrial genomes and species boundaries. Molecular Ecology. 26: 2212-2236.
2016
Rockenbach K, Havird JC, Monroe JG, Triant DA, Taylor DR, Sloan DB. 2016. Positive selection in rapidly evolving plastid-nuclear enzyme complexes. Genetics. 204: 1507-1522.
Havird JC, Sloan DB. 2016. The roles of mutation, selection, and expression in determining relative rates of evolution in mitochondrial vs. nuclear genomes. Molecular Biology and Evolution. 33: 3042-3053.
Harrison TD, Ruiz J, Sloan DB, Ben-Hur A, Boucher C. 2016. aPPRove: an HMM-based method for accurate prediction of RNA-pentatricopeptide repeat protein binding events. PLoS One. 11: e0160645.
Havird JC, Fitzpatrick S, Funk WC, Kronenberger J, Angeloni LM, Sloan DB. 2016. Sex, mitochondria, and genetic rescue. Trends in Ecology and Evolution. 31: 96-99.
Warren JM, Simmons MP, Wu Z, Sloan DB. 2016. Linear plasmids and the rate of sequence evolution in plant mitochondrial genomes. Genome Biology and Evolution. 8: 364-374.
Simmons MP, Sloan DB, Gatesy J. 2016. The effects of subsampling gene trees on coalescent methods applied to ancient divergences. Molecular Phylogenetics and Evolution. 97: 76-89.
Sloan DB, Wu Z. 2016. Molecular evolution: The perplexing diversity of mitochondrial RNA editing systems. Current Biology. 26: R22-R24.
2015
Havird JC, Whitehill NS, Snow CD, Sloan DB. 2015. Conservative and compensatory evolution in oxidative phosphorylation complexes of angiosperms with highly divergent rates of mitochondrial genome evolution. Evolution. 69: 3069-3081.
Moran NA, Sloan DB. 2015. The hologenome concept—helpful or hollow? PLoS Biology. 13: e1002311.
Wu Z, Stone JD, Štorchová H, Sloan DB. 2015. High transcript abundance, RNA editing, and small RNAs in intergenic regions within the massive mitochondrial genome of the angiosperm Silene noctiflora. BMC Genomics. 16: 938.
Sloan DB, Fields PD, Havird JC. 2015. Mitonuclear linkage disequilibrium in human populations. Proceedings of the Royal Society B. 282: 20151704.
Wu Z, Cuthbert JM, Taylor DR, Sloan DB. 2015. The massive mitochondrial genome of the angiosperm Silene noctiflora is evolving by gain or loss of entire chromosomes. Proceedings of the National Academy of Sciences. 112: 10185-10191.
Sloan DB. 2015. Using plants to elucidate the mechanisms of cytonuclear co-evolution. New Phytologist. 205: 1040-1046.
2014
Barnard-Kubow KB, Sloan DB, Galloway LF. 2014. Correlation between sequence divergence and polymorphism reveals similar evolutionary mechanisms acting across multiple timescales in a rapidly evolving plastid genome. BMC Evolutionary Biology. 14: 1.
Sloan DB, Wu Z. 2014. History of plastid DNA insertions reveals weak deletion and AT mutation biases in angiosperm mitochondrial genomes. Genome Biology and Evolution. 6: 3210-3221.
Sloan DB, Nakabachi A, Richards S, Qu J, Murali SC, Gibbs RA, Moran NA. 2014. Parallel histories of horizontal gene transfer facilitated extreme reduction of endosymbiont genomes in sap-feeding insects. Molecular Biology and Evolution. 31: 857-871.
Sloan DB, Triant DA, Wu M, Taylor DR. 2014. Cytonuclear interactions and relaxed selection accelerate sequence evolution in organelle ribosomes. Molecular Biology and Evolution. 31: 673-682.
Sloan DB, Triant DA, Forrester NJ, Bergner LM, Wu M, Taylor DR. 2014. A recurring syndrome of accelerated plastid genome evolution in the angiosperm tribe Sileneae (Caryophyllaceae). Molecular Phylogenetics and Evolution. 72: 82-89.
Pre-CSU (2013 and Earlier)
Sloan DB. 2013. One ring to rule them all? Genome sequencing provides new insights into the ‘master circle’ model of plant mitochondrial DNA structure. New Phytologist. 200: 978-985.
Sloan DB, Bennett GM, Engel PE, Williams D, Ochman H. 2013. Disentangling associated genomes. Methods in Enzymology. 531: 445-464.
Sloan DB, Moran NA. 2013. The evolution of genomic instability in the obligate endosymbionts of whiteflies. Genome Biology and Evolution. 5: 783-793.
Wilton PR, Sloan DB, Logsdon JM, Doddapaneni H, Neiman M. 2013. Characterization of transcriptomes from sexual and asexual lineages of a New Zealand snail (Potamopyrgus antipodarum). Molecular Ecology Resources. 13: 289-294.
Sloan DB, Müller K, McCauley DE, Taylor DR, Štorchová H. 2012. Intraspecific variation in mitochondrial genome sequence, structure, and gene content in Silene vulgaris, an angiosperm with pervasive cytoplasmic male sterility. New Phytologist. 196: 1228-1239.
Sloan DB, Moran NA. 2012. Endosymbiotic bacteria as a source of carotenoids in whiteflies. Biology Letters. 8: 986-989.
Sloan DB, Moran NA. 2012. Genome reduction and co-evolution between the primary and secondary bacterial symbionts of psyllids. Molecular Biology and Evolution. 29: 3781-3792.
Raghavan R, Sloan DB, Ochman H. 2012. Antisense transcription is pervasive but rarely conserved in enteric bacteria. mBio. 3: e00156-12
Sloan DB, Alverson AJ, Wu M, Palmer JD, Taylor DR. 2012. Recent acceleration of plastid sequence and structural evolution coincides with extreme mitochondrial divergence in the angiosperm genus Silene. Genome Biology and Evolution. 4: 294-306.
Sloan DB, Alverson AJ, Chuckalovcak JP, Wu M, McCauley DE, Palmer JD, Taylor DR. 2012. Rapid evolution of enormous, multichromosomal genomes in flowering plant mitochondria with exceptionally high mutation rates. PLoS Biology. 10: e1001241.
Mower JP, Sloan DB, Alverson AJ. 2012. Plant mitochondrial diversity – the genomics revolution. Plant Genome Diversity vol. 1, Wendel JF (ed.) Springer-Verlag, Vienna. pp. 123-144.
Sloan DB, Keller SR, Berardi AE, Sanderson BJ, Karpovich JF, Taylor DR. 2012. De novo transcriptome assembly and polymorphism detection in the flowering plant Silene vulgaris (Caryophyllaceae). Molecular Ecology Resources. 12: 333-343.
Rautenberg A, Sloan DB, Aldén V, Oxelman B. 2012. Phylogenetic relationships of Silene multinervia (Caryophyllaceae) and Silene section Conoimorpha. Systematic Botany. 37: 226-237.
Sloan DB, Taylor DR. 2012. Evolutionary rate variation in organelle genomes: the role of mutational processes. In: Bullerwell CE (ed.). Organelle Genetics: Evolution of Organelle Genomes and Gene Expression. Springer-Verlag, Berlin. pp. 123-146.
Alverson AJ, Zhuo S, Rice DW, Sloan DB, Palmer JD. 2011. The mitochondrial genome of the legume Vigna radiata and the analysis of recombination across short mitochondrial repeats. PLoS One. 6: e16404.
Sloan DB, Alverson AJ, Štorchová H, Palmer JD, Taylor DR. 2010. Extensive loss of translational genes in the structurally dynamic mitochondrial genome of Silene latifolia. BMC Evolutionary Biology. 10: 274.
Sloan DB, Taylor DR. 2010. Testing for selection on synonymous sites in plant mitochondrial genomes: the role of codon bias and RNA editing. Journal of Molecular Evolution. 70: 479-491.
Sloan DB, MacQueen AH, Alverson AJ, Palmer JD, Taylor DR. 2010. Extensive loss of RNA editing sites in rapidly evolving Silene mitochondrial genomes: Selection vs. retroprocessing as the driving force. Genetics. 185: 1369-1380.
Sloan DB, Panjeti VG. 2010. Evolutionary feedbacks between reproductive mode and mutation rate exacerbate the paradox of sex. Evolution. 64: 1129-1135.
Sloan DB, Oxelman B, Rautenberg A, Taylor DR. 2009. A phylogenetic analysis of mitochondrial substitution rate variation in the angiosperm tribe Sileneae (Caryophyllaceae). BMC Evolutionary Biology. 9: 260.
Sloan DB, Barr CM, Olson MS, Keller SR, Taylor DR. 2008. Evolutionary rate variation at multiple levels of biological organization in plant mitochondrial DNA. Molecular Biology and Evolution. 25: 243-246.
Sloan DB, Giraud T, Hood ME. 2008. Maximized virulence in a sterilizing pathogen: the anther-smut fungus and its co-evolved hosts. Journal of Evolutionary Biology. 21: 1544-1554.
Bret-Harte MS, Mack MC, Goldsmith GR, Sloan DB, DeMarco J, Shaver GR, Ray PM, Biesinger Z, Chapin FS. 2008. Plant functional types do not predict biomass responses to removal and fertilization in Alaskan tussock tundra. Journal of Ecology. 96: 713-726.
Pillitteri LJ, Sloan DB, Bogenschutz NL, Torii KU. 2007. Termination of asymmetric cell division and differentiation of stomata. Nature. 445: 501-505.
Antonovics J, Abbate JL, Baker CE, Daley D, Hood ME, Jenkins CE, Johnson LJ, Murray JJ, Panjeti VG, Rudolf VHW, Sloan DB, Vondrasek J. 2007. Evolution by any other name: Antibiotic resistance and avoidance of the E-word. PLoS Biology. 5: e30.
Barr CM, Keller SR, Ingvarsson PK, Sloan DB, Taylor DR. 2007. Variation in polymorphism and mutation rate among mitochondrial genes in Silene vulgaris. Molecular Biology and Evolution. 24: 1783-1791.
McCormick MK, Whigham DF, Sloan DB, O'Malley K, Hodkinson B. 2006. Orchid-fungal fidelity: a marriage meant to last? Ecology. 87: 903-911.
Heschel MS, Sultan SE, Glover S, and Sloan DB. 2004. Population differentiation and plastic responses to drought stress in the generalist annual, Polygonum persicaria. International Journal of Plant Science. 165: 817-824.