Holm, K.M., Koepfli, K.-P., Pukazhenthi, B.S., Ratan, A., Fryxell, K.J., Pham, M., Weisz, D., Dudchenko, O., Aiden, E.L., Lim, H.C., 2025. Chromosome-length genome assembly of the critically endangered Mountain bongo (Tragelaphus eurycerus isaaci): A resource for conservation and comparative genomics. G3 https://doi.org/10.1093/g3journal/jkaf109
Lim, H.C., Bennett, K.F.P., Justyn, N.M., Powers, M.J., Long, K.M., Kingston, S.E., Lindsay, W.R., Pease, J.B., Fuxjager, M.J., Bolton, P.E., Balakrishnan, C.N., Day, L.B., Parsons, T.J., Brawn, J.D., Hill, G.E., Braun, M.J., 2024. Sequential introgression of a carotenoid processing gene underlies sexual ornament diversity in a genus of manakins. Science Advances 10, eadn8339.
Amiri, N.*, M. M. Keady**, and H. C. Lim. 2023. Honey bees and bumble bees occupying the same landscape have distinct gut microbiomes and amplicon sequence variant-level responses to infections. PeerJ. 11:e15501.
Lim, H. C., D. H. Lambrecht**, R. E. Forkner, and T. Roulston. 2023. Minimal sharing of nosematid and trypanosomatid parasites between honey bees and other bees, but extensive sharing of Crithidia between bumble and mason bees. Journal of Invertebrate Pathology 198:107933.
Shakya, S. B., A. Alexander, H. C. Lim, J. D. Manthey, D. Prawiradilaga, et al. 2023. Demographic history of a complex polymorphism in populations of the Oriental Dwarf Kingfisher (Ceyx erithaca/rufidorsa) of Southeast Asia. Ibis. https://doi.org/10.1111/ibi.13207
Clark, J. D.**, F. M. Benham, J. E. Maldonado, D. Luther, and H. C. Lim. 2022. Maintenance of local adaptation despite gene flow in a coastal songbird. Evolution 76:1481-1494.
Keady, M. M.**, N. Prado, H. C. Lim, J. Brown, S. Paris, et al. 2021. Clinical health issues, reproductive hormones, and metabolic hormones associated with gut microbiome structure in African and Asian elephants. Animal Microbiome 3:85.
Cassin-Sackett, L., M. G. Campana, N. R. McInerney, H. C. Lim, N. A. S. Przelomska, et al. 2021. Genetic structure and population history in two critically endangered Kaua‘i honeycreepers. Conservation Genetics 22:601-614.
Bennett, K. F. P., H. C. Lim, and M. J. Braun. 2021. Sexual selection and introgression in avian hybrid zones: Spotlight on Manacus. Integrative and Comparative Biology 61:1291-1309.
Feng, S., J. Stiller, Y. Deng, J. Armstrong, Q. Fang, et al. 2020. Dense sampling of bird diversity increases power of comparative genomics. Nature 587:252-257
Bragg, M.**, E. W. Freeman, H. C. Lim, N. Songsasen, and C. R. Muletz-Wolz. 2020. Gut Microbiomes Differ Among Dietary Types and Stool Consistency in the Captive Red Wolf (Canis rufus). Frontiers in Microbiology 11:590212.
Kang, J.**, A. M. Ismail, S. Dehghan, J. Rajaiya, M. W. Allard, H. C. Lim, D. W. Dyer, J. Chodosh, and D. Seto. 2020. Genomics-based re-examination of the taxonomy and phylogeny of human and simian Mastadenoviruses: an evolving whole genomes approach, revealing putative zoonosis, anthroponosis, and amphizoonosis. Cladistics 36:358-373.
Parker, L. D., M. T. R. Hawkins, M. Camacho-Sanchez, M. G. Campana, J. A. West-Roberts, et al. 2020. Little genetic structure in a Bornean endemic small mammal across a steep ecological gradient. Molecular Ecology 29:4074-4090.
Lim, H. C., S. B. Shakya, M. G. Harvey, R. G. Moyle, R. C. Fleischer, M. J. Braun, and F. H. Sheldon. 2020. Opening the door to greater phylogeographic inference in continental Southeast Asia: Comparative study of five co-distributed rainforest bird species using target capture and historical DNA. Ecology and Evolution 10:3222-3247.
Sheldon, F. H., H. C. Lim, F. Benham, M. L. Brady, C. E. Brown, et al. 2019. Ornithological expeditions to Sarawak, Malaysian Borneo, 2007-2017. Occasional Papers of the Museum of Natural Science, Louisiana State University 90:1-11.
Shakya, S. B., H. C. Lim, R. G. Moyle, M. A. Rahman, M. Lakim, and F. H. Sheldon. 2019. A cryptic new species of bulbul from Borneo. Bulletin of the British Ornithologists’ Club 139:46-55.
Drovetski, S. V., M. O’Mahoney, E. J. Ransome, K. O. Matterson, H. C. Lim, R. T. Chesser, and G. R. Graves. 2018. Spatial organization of the gastrointestinal microbiota in urban Canada geese. Scientific Reports 8:3713.
Lim, H. C., D. F. Gawin, S. B. Shakya, M. G. Harvey, M. A. Rahman, and F. H. Sheldon. 2017. Sundaland’s east-west rain forest population structure: Variable manifestations in four polytypic bird species examined using RAD-Seq and plumage analyses. Journal of Biogeography 44:2259-2271
Lim, H.C. and M.J. Braun. 2016. High-throughput SNP genotyping of historical and modern samples of five bird species via sequence capture of ultraconserved elements. Molecular Ecology Resources (Sequence Capture Special Issue) 16:1204-23
Cameron, S. A., H.C. Lim, J. D. Lozier, M.A. Duennes and R.W. Thorp. 2016. A test of the invasive pathogen hypothesis of bumble bee decline in North America. Proceedings of the National Academy of Sciences 113:4386-91
Sheldon, F.H., H.C. Lim and R.G. Moyle. 2015. Return to the Malay Archipelago: the biogeography of Sundaic rainforest birds. Journal of Ornithology (International Ornithological Congress Special Issue) 156:91-113
Peterson, A. T., R. G. Moyle, F. Lei, L. C. Campillo, P. A. Hosner, L. B. Klicka, H. C. Lim, A. S. Nyari, Y. QU, S. Reddy, F. H. Sheldon, and F. Zou. 2015. Avian evolution and speciation in the Southeast Asian tropics. Current Zoology 61:898-900.
Lim, H.C., C.-C. Chu, M.J. Seufferheld, S.A. Cameron. 2015. Deep sequencing and ecological characterization of gut microbial communities of diverse bumble bee species. PLoS ONE 10: e0118566.
Sheldon, F., H. C. Lim, and R. Moyle. 2015. Return to the Malay Archipelago: the biogeography of Sundaic rainforest birds. Journal of Ornithology 156:91-113.
Chua, V, Q. Phillips, H.C. Lim et al. 2015. Phylogeography of three endemic birds of Maratua Island, potential archive of Bornean biogeography. Raffles Bulletin of Zoology 63: 259–269.
Lim, H. C., F. Zou, and F. H. Sheldon. 2015. Genetic differentiation in two widespread, open-forest bird species of Southeast Asia (Copsychus saularis and Megalaima haemacephala): Insights from ecological niche modeling Current Zoology 61:922-934.
Lim, H.C. and M.R.C. Posa. 2014. Distribution and prey of migratory shorebirds on the northern coastline of Singapore. Raffles Bulletin of Zoology 62:701-717.
Lim, H. C., V. L. Chua, P. M. Benham, C. H. Oliveros, M. A. Rahman, R. G. Moyle and F. H. Sheldon. 2014. Divergence history of the Rufous-tailed Tailorbird (Orthotomus sericeus) of Sundaland: Implications for the biogeography of Palawan and the taxonomy of island species in general. Auk 131:629-642.
Gawin, D. F., M. A. Rahman, M. F. S. Ramji, B. T. Smith, H. C. Lim, R. G. Moyle, and F. H. Sheldon. 2014. Patterns of avian diversification in Borneo: The case of the endemic Mountain Black-eye (Chlorocharis emiliae). Auk 131:86-99.
Sheldon, F. H., C. H. Oliveros, S. S. Taylor, B. McKay, H. C. Lim, M. A. Rahman, H. Mays, and R. G. Moyle. 2012. Molecular phylogeny and insular biogeography of the lowland tailorbirds of Southeast Asia (Cisticolidae: Orthotomus) 2012. Molecular Phylogenetics and Evolution 65:54-63.
Chong, K. Y., S. Teo, B. Kurukulasuriya, Y. F. Chung, S. Rajathurai, H. C. Lim, and H. T. W. Tan. 2012. Decadal changes in urban bird abundance in Singapore. Raffles Bulletin of Zoology Supp. No. 25:181-188.
Moyle, R. G., S. S. Taylor, C. H. Oliveros, H. C. Lim, et al. 2011. Diversification of an insular Southeast Asian clade: Phylogenetic relationships of the Spiderhunters (Aves: Nectariniidae). Auk 128:777-788.
Lim, H. C., and F.H. Sheldon. 2011. Multilocus analysis of the evolutionary dynamics of rainforest bird populations in Southeast Asia. Molecular Ecology 20:3414-3438. (Cover page article)
Lim, H. C., M. A. Rahman, S. L. H. Lim, R. G. Moyle, et al. 2011. Revisiting Wallace's haunt: Coalescent simulations and comparative niche modeling reveal historical mechanisms that promoted avian population divergence in the Malay Archipelago. Evolution 65:321-334.
Yong, D. L., L. Qie, N. S. Sodhi, L. P. Koh, K. S.-H. Peh, T. M. Lee, H. C. Lim, and S. L.-H. Lim 2011. Do insectivorous bird communities decline on land-bridge forest islands in Peninsular Malaysia? Journal of Tropical Ecology 27:1-14.
Hosner, P. A., F. H. Sheldon, H. C. Lim, and R. G. Moyle. 2010. Phylogeny and biogeography of the Asian trogons (Aves: Trogoniformes) inferred from nuclear and mitochondrial DNA sequences. Molecular Phylogenetics and Evolution 57:1219-1225.
Lim, H. C., F. S. Zou, S. S. Taylor, B. D. Marks, et al. 2010. Phylogeny of magpie-robins and shamas (Aves: Turdidae: Copsychus and Trichixos): implications for island biogeography in Southeast Asia. Journal of Biogeography 37:1894-1906.
Lim, H. C., F. H. Sheldon, and R. G. Moyle. 2010. Extensive color polymorphism in the Southeast Asian Oriental dwarf kingfisher Ceyx erithaca: a result of gene flow during population divergence? Journal of Avian Biology 41:305-318.
Lim, H. C., and N. S. Sodhi. 2009. Space use and habitat selection of house crows in a tropical urban environment: A radio-tracking study. Raffles Bulletin of Zoology 57:561-568.
Sheldon, F. H., H. C. Lim, J. Nais, M. Lakim, et al. 2009. Observations on the ecology, distribution and biogeography of forest birds in Sabah, Malaysia. Raffles Bulletin of Zoology 57:577-586.
Sheldon, F. H., D. J. Lohman, H. C. Lim, F. Zou, et al. 2009. Phylogeography of the magpie-robin species complex (Aves: Turdidae: Copsychus) reveals a Philippine species, an interesting isolating barrier and unusual dispersal patterns in the Indian Ocean and Southeast Asia. Journal of Biogeography 36:1070-1083.
Sodhi, N. S., D. Astuti, A. C. Diesmos, P. Ericson, N. Fernandopulle, et al. 2007. Barcoding Indo-Malayan birds. Raffles Bulletin of Zoology 55:397-398.
Zou, F., H. C. Lim, B. D. Marks, R. G. Moyle, and F. H. Sheldon. 2007. Molecular phylogenetic analysis of the gray-cheeked fulvetta (Alcippe morrisonia) of China and Indochina: a case of remarkable genetic divergence in a "species". Molecular Phylogenetics and Evolution 44:165-174.
Lim, H. C. and N. S. Sodhi. 2004. Responses of avian guilds to urbanization in a tropical city. Landscape and Urban Planning 66:199-215.
Lim, H. C., N. S. Sodhi, B. W. Brook, and M. C. K. Soh. 2003. Undesirable aliens: factors determining the distribution of three invasive bird species in Singapore. Journal of Tropical Ecology 19:685-695.
Brook, B. W., N. S. Sodhi, M. C. K. Soh, and H. C. Lim. 2003. Abundance and projected control of invasive house crows in Singapore. Journal of Wildlife Management 67:808-817..