- + Graduate student co-author
- * Undergraduate student co-author
Hoch H, Porter ML, Slay CM, Slay ME, Steck M, and Chong RA. (2024) From the dark side of Paradise: a new natural replication of cave planthopper evolution from Hawaiian lava tubes (Hemiptera: Fulgoromorpha: Cixiidae). Zoological Journal of the Linnean Society zlad198. https://doi.org/10.1093/zoolinnean/zlad198
Hanauer DI, Zhang T, Graham MJ, et. al. Adams SD, Ahumada-Santos YP, Alvey RM, Antunes MS, Ayuk MA, Elena Báez-Flores M, Bancroft CT, Bates TC, Bechman MJ, Behr E, Beyer AR, Bortz RL, Bowder DM, Briggs LA, Brown-Kennerly V, Buckholt MA, Bullock SK, Butela KA, Byrum CA, Caruso SM, Chia CP, Chong RA, Chung H-M, Clase KL, Coleman ST, Parks Collins D, Conant SB, Condon BM, Connerly PL, Connors BJ, Cook-Easterwood JE, Crump KE, D’Elia T, Dennis MK, DeVeaux LC, Diacovich L, Duffy I, Edgington NP, Edwards DC, Egwuatu TOG, Eivazova ER, Fallest-Strobl PC, Fillman CL, Findley AM, Fisher E, Fisher MR, Fogarty MP, Freise AC, Frost VJ, Gainey MD, Garcia Costas AM, Garza AA, Gavin HE, Ghittoni R, Gibb B, Golebiewska UP, Grinath AS, Gurney SMR, Hare RF, Heninger SG, Hinz JM, Hughes LE, Jayachandran P, Johnson KC, Johnson AA, Kanther M, Kenna M, Kirkpatrick BL, Klyczek KK, Kohl KP, Kuchka M, LaPeruta AJ, Lee-Soety JY, Lewis LO, Lindberg HM, Madden JA, Markov SA, Mastropaolo MD, Mathur V, McClory SP, Merkhofer EC, Merkle JA, Michael SF, Mitchell JC, Molloy SD, Monti DL, Mussi MA, Nance H, Nieto-Fernandez FE, Nissen JC, Nsa IY, O’Donnell MG, Page ST, Panagakis A, Parra-Unda JR, Pelletier TA, Perez Morales TG, Peters NT, Phuntumart V, Pollenz RS, Preuss ML, Puthoff DP, Raifu MK, Reyna NS, Rinehart CA, Rocheleau JM, Rossier O, Rudner AD, Rueschhoff EE, Ryan A, Saha S, Shaffer CD, Smith MAV, Sprenkle AB, Strong CL, Sunnen CN, Tarbox BP, Temple L, Thoemke KR, Thomas MA, Tobiason DM, Tolsma SS, Garcia JT, Valentine MS, Vazquez E, Ward RE, Ward CM, Ware VC, Warner MH, Washington JM, Westholm DE, Wheaton KA, Wilkes BM, Williams EC, Biederman WH, Cresawn SG, Heller DM, Jacobs-Sera D, Hatfull GF, Asai DJ and Sivanathan V (2023) Models of classroom assessment for course- based research experiences. Front. Educ. 8:1279921. https://doi.org/10.3389/feduc.2023.1279921
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. (2023) Species delimitation, phylogenomics, and biogeography of Sulawesi flying lizards: a diversification history complicated by ancient hybridization, cryptic species, and failed speciation. Systematic Biology 72(4):885-911. https://doi.org/10.1093/sysbio/syad020
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. https://doi.org/10.1093/iob/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. (2022) Genome Sequence of Arthrobacter Phage NathanVaag. Microbial Resources Announcements https://doi.org/10.1128/mra.00940-22
Porter ML, Lutz H, Steck M, and Chong RA. (2022) The complete mitochondrial genomes and phylogenetic analysis of two Nycteribiidae bat flies (Diptera: Hippoboscoidea). Mitochondrial DNA Part B, 7(8): 1486-1488. DOI: 10.1080/23802359.2022.2107450
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 Announcements 11:e00439-22 https://doi.org/10.1128/mra.00439-22
(2022) Complete mitochondrial genomes and phylogenetic analysis of the Hawaiian planthoppers Iolania perkinsi and Oliarus cf. filicicola (Hemiptera: Cixiidae). Mitochondrial DNA Part B, 7:6, 1015-1017, DOI: 10.1080/23802359.2022.2080596
Chong RA, Park H*, and Moran NA. (2019) Genome evolution of the obligate symbiont Buchnera aphidicola. Molecular 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. (2019) One hundred mitochondrial genomes of cicadas. Journal of Heredity 110(2):247-256 https://doi.org/10.1093/jhered/esy068
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 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
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