Publications

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Richards EJ, Brown JM, Barley AJ, Chong RA, and Thomson RC. (2018) Variation across mitochondrial gene trees provides evidence for systematic error: How much gene tree variation is biological? Systematic Biology doi.org/10.1093/sysbio/syy013

Chong RA and Moran NA. (2018) Evolutionary loss and replacement of an obligate endosymbiont in aphids. The ISME Journal doi:10.1038/s41396-017-0024-6

Chong RA and Mueller RL. (2017) Polymorphic duplicate genes and persistent non-coding sequences reveal heterogeneous patterns of mitochondrial DNA loss in salamanders. BMC Genomics 18:992

Bennett GM and Chong RA. (2017) Genome-wide transcriptional dynamics in the companion bacterial symbionts of the glassy-winged sharpshooter (Cicadellidae: Homalodisca vitripennis) reveal differential gene expression in bacteria occupying multiple host organs. G3: Genes, Genomes, Genetics 7(9): 3073-3082

Chong RA and Moran NA. (2016) Intraspecific genetic variation in hosts affects regulation of obligate heritable symbionts. Proceedings of the National Academy of Sciences USA 113(46): 13114-13119

Frahry MB*, Sun C, Chong RA, and Mueller RL. (2015) Low levels of LTR retrotransposon deletion by ectopic recombination in the gigantic genomes of salamanders. Journal of Molecular Evolution 80(2): 120-129 (* = undergraduate co-author)

Leaché AD, Wagner P, Linkem C, Böhme W, Papenfuss TJ, Chong RA, Lavin B, Bauer AM, Nielsen S, Greenbaum E, Rodel MO, Schmitz A, LeBreton A, Ineich I, Chirio L, Ofori-Boateng C, Eniang E, Baha El Din S, Lemmon A, and Burbrink FT. (2014) A hybrid phylogenetic-phylogenomic approach for species tree estimation in African Agama lizards with applications to biogeography, character evolution, and diversification. Molecular Phylogenetics and Evolution 79: 215-230

Chong RA and Mueller RL. (2013) Evolution along the mutation gradient in the dynamic mitochondrial genome of salamanders. Genome Biology and Evolution 5(9): 1652-1660

Chong RA and Mueller RL. (2013) Low metabolic rates in salamanders are correlated with weak selective constraints on mitochondrial genes. Evolution 67(3): 894-899 (F1000 Prime recommended)

Sun C, Shepard DB, Chong RA, Lopez-Arriaza J, Hall K, Castoe TA, Feschotte C, Pollock DD, and Mueller RL. (2012) LTR retrotransposons contribute to genomic gigantism in plethodontid salamanders. Genome Biology and Evolution 4(2): 168-183

Swei A, Rowley JJL, Rödder D, Diesmos MLL, Diesmos AC, Briggs CJ, Brown R, Cao TT, Cheng TL, Chong RA, Han B, Hero JM, Hoang HD, Kusrini MD, Le DTT, McGuire JA, Meegaskumbura M, Min MS, Mulcahy DG, Neang T, Phimmachak S, Rao DQ, Reeder NM, Schoville SD, Sivongxay N, Srei N, Stöck M, Stuart BL, Torres LS, Tran DTA, Tunstall TS, Vietes D, and Vredenburg VT. (2011) Is chytridiomycosis an emerging infectious disease in Asia? PLoS ONE 6(8): e23179

Leaché AD, Chong RA, Papenfuss TJ, Wagner P, Böhme W, Schmitz A, Rödel MO, LeBreton, M, Ineich I, Chirio L, Bauer A, Eniang EA, and Baha El Din S. (2009) Phylogeny of the genus Agama based on mitochondrial DNA sequence data. Bonner zoologische Beiträge 56: 273-278