Becky Chong

Rebecca A. Chong

Associate Professor

2014 Ph.D., Zoology, Dept. of Biology, Colorado State University
2007 B.A., Integrative Biology, Dept. of Integrative Biology, University of California Berkeley

Genome evolution, symbiosis, biodiversity, Hawaiian lava tubes

See Research


  • Graduate student co-author
  • * Undergraduate student co-author

McGuire JA, Huang X, Reilly SB, Iskandar DT, Werning S, Chong RA, Lawalata S, Linkem CW, Brown RM, Evans BJ, Riyanto A, Arida E, Hamidy A, Supriatna J, Andayani N, and Hall R. Species delimitation, phylogenomics, and biogeography of Sulawesi flying lizards: a diversification history complicated by ancient hybridization, cryptic species, and failed speciation. Systematic Biology (in press)

Mueller RL, Cressler CE, Schwartz RS, Chong RA, and Butler MB. Metamorphosis imposes variable constraints on genome expansion through effects on development. Integrative Organismal Biology 5(1): obad015.

Gossett JM+, Porter ML, Vasquez Y, Bennett GM, and Chong RA. Genomic comparisons reveal selection pressure and functional variation between endosymbionts of cave-adapted and epigean Hawaiian planthoppers. Genome Biology Evolution 15(3): evad031

Cao L, Tan H, Zheng H, Wang Y, Chen J, Kuang H, Chong RA, Hu F, Sun W, and Sun C. Population structure, demographic history and adaptation of giant honeybees in China revealed by population genomic data. Genome Biology Evolution 15(3): evad025

Chong RA, Cosse CM*,  Gaytan V*,  Green DS*,  Kane CJ*,  Kasal KA*,  Kon ZK*,  Maxwell RE*,  Olaru V*,  Pham TD*,  Precourt MF*,  Romero JR*,  Rothschild WJ*,  Sales SN*,  Sensano TD*,  Simko WE*,  Smith IJ*,  Toor MA*,  Wilson AR*, and Porter ML. Genome Sequence of Arthrobacter Phage NathanVaag. Microbial Resources Announcements

Porter ML, Steck M, Lutz H, and Chong RA. (2022) The complete mitochondrial genomes and phylogenetic analysis of two Nycteribiidae bat flies (Diptera: Hippoboscoidea). Mitochondrial DNA Part B: Resources 7(8): 1486-1488

Chong RA, SEA-PHAGES students University of Hawaiʻi Mānoa*, Donachie SP, Reed FA, and Porter ML. (2022) Genome Sequence of Arthrobacter globiformis Phage KeAlii from Hawaiʻi. Microbial Resources Announcements11:e00439-22

Chong RA, Steck M, and Porter ML. (2022) Complete mitochondrial genomes and phylogenetic analysis of the Hawaiian planthoppers Iolania perkinsi and Oliarus cf filicicola (Hemiptera: Cixiidae). Mitochondrial DNA Part B: Resources 7(6):1015-1017.

Chong RA, Park H, and Moran NA. (2019) Genome evolution of the obligate symbiont Buchnera aphidicolaMolecular Biology and Evolution doi:10.1093/molbev/msz082

Łukasik P, Chong RA, Nazario K, Matsuura Yu, Bublitz D, Campbell M, Meyer M, Van Leuven J, Pessacq P, Veloso C, Simon C, and J McCutcheon. One hundred mitochondrial genomes of cicadas. Journal of Heredity 110(2):247-256

Moran NA and Chong RA. “Endosymbiosis.” Oxford Bibliographies in Evolutionary Biology. Ed. Karin Pfennig. New York: Oxford University Press, September 25, 2018. DOI: 10.1093/OBO/9780199941728-0114

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

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