Publications

(* corresponding authors; bold: our lab members)

2025

  1. Chen, C. Y., Kuo, H. C., Fang, Y. T., Lu, C. W., Chen, S. K., & Hung, C. M.* (2025). Microbiota-gut-brain axis in avian parenting: gut microbiome associates with nest-construction behavior and neural gene expression in a songbird. Animal Microbiome, 7(1), 120. https://doi.org/10.1186/s42523-025-00486-w
  2. Yang, Y.-W., Hsu, B.-Y., Guo, J.-C., Hung, C.-M.* (2025) Relative brain size explains migratory/resident tendency in birds: partial altitudinal migration in Asian house martins. Journal of Animal Ecology, 94, 2338-2349. https://doi.org/10.1111/1365-2656.7094, 2338-234 
  3. Chou, C.-C., Tuanmu, M.-N.*, Hung, C.-M.* (2025) Egg mass drives the evolution of bird nest architecture. Proceedings of the Royal Society B, 292, 20251445. https://doi.org/10.1098/rspb.2025.1445
  4. Wang, Z., Cui, N., Hung, C.-M., Li, S.-H. and Dong, F*. (2025). A 150‐Year avian extinction debt forewarns a global species crisis and highlights conservation opportunities. Conservation Letters, 18, e13078. https://doi.org/10.1111/conl.13078

2024

  1. Guo, J.-C., Shaner, P.-J.L.*, Hung, C.-M.* (2024) A 3D modelling approach to measuring structural characteristics of bird nest interiors. Methods in Ecology and Evolution, 15, 2226-2233. https://doi.org/10.1111/2041-210X.14448
  2. Fang, Y.-T., Kuo, H.-C., Chen, C.-Y., Chou, S.-J., Lu, C.-W. & Hung, C.-M.* (2024) Brain gene regulatory networks coordinate nest construction in birds. Molecular Biology & Evolution, 41(7), msae125. https://doi.org/10.1093/molbev/msae125
  3. Kamali, K., Nazarizadeh, M., Fatemizadeh, F., Salmabadi, S., Hung, C.-M.* & Kaboli, M.* (2024) Integrating phylogenetic, phylogeographic, and morphometric analyses to reveal cryptic lineages within the genus Asaccus (Reptilia: Squamata: Phyllodactylidae) in Iran. BMC Zoology, 9, 12. https://doi.org/10.1186/s40850-024-00203-1
  4. Chan, Y.-F., Lu, C.-W., Kuo, H.-C.* & Hung, C.-M.* (2024) A chromosome-level genome assembly of the Asian house martin implies potential genes associated with the feathered-foot trait. G3-Genes Genomes Genetics, jkae077. https://doi.org/10.1093/g3journal/jkae077

2023

  1. Chia, S.-Y., Fang, Y.-T., Su, Y.-T., Tsai, P.-Y., Hsieh C., Tsao, S.-H., Juang, J.-Y., Hung, C.-M.* & Tuanmu, M.-N.* (2023) A global database of bird nest traits. Scientific Data, 10, 923. https://doi.org/10.1038/s41597-023-02837-1
  2. Lu, C.-W., Huang, S.-T., Cheng, S.-J., Lin, C.-T., Hsu, Y.-C., Yao, C.-T., Dong, F, Hung, C.-M.* & Kuo, H.-C.* (2023) Genomic architecture underlying morphological and physiological adaptation to high elevation in a songbird. Molecular Ecology, 32, 2234-2251. https://doi.org/10.1111/mec.16875
  3. Kuo, H.-C., Yao, C.-T., Liao, B.-Y., Weng, M.-P., Dong, F., Hsu, Y.-C. & Hung, C.-M.* (2023) Weak gene-gene interaction facilitates the evolution of gene expression plasticity. BMC Biology, 21, 57. https://doi.org/10.1186/s12915-023-01558-6
  4. Ku, Y.-C., Chen, Y.-C., Hung, C.-M. & Ng, C.- S.* (2023) The genetic variation of a mitochondrial and two behaviour-related genes in invasive African Sacred Ibis (Threskiornis aethiopicus) populations in Taiwan. IBIS, 165, 647-662. https://doi.org/10.1111/ibi.13146

2022

  1. Guo, J.-C., Tsai, J.-S., Wang, J.-S., Lin, Y.-W., Shaner, P.-J.* & Hung, C.-M.* (2022) The role of a synanthropic bird in the nest niche expansion of a secondary cavity nester to man-made structures. Ecology & Evolution, 12, e9188. https://doi.org/10.1002/ece3.9188
  2. Hung, C.-M. †, Tsao, S.-H. †, Chiang, P.-L., Wu, S.-P., Tuanmu M.-N.* & Juang, J.-Y.* (2022) Functional connections between bird eggshell stiffness and nest characteristics through risk of egg collision in nests. Ecology Letters, 25, 1421-1431. († equal contributors). https://doi.org/10.1111/ele.14001
  3. Lu, C.-W., Yao, C.-T., & Hung, C.-M.* (2022). Domestication obscures genomic estimates of population history. Molecular Ecology, 31, 752-766. https://doi.org/10.1111/mec.16277
  4. Fang, Y.-T., Yao, C.-T., Hsu, Y.-C. & Hung, C.-M.* (2022) Elevational plumage divergence in the Rufous-capped Babbler on a mountainous island. IBIS, 164, 151-167. https://doi.org/10.1111/ibi.13009

2021

  1. Wang, J.-S.†, Tuanmu, M.-N.† & Hung, C.-M.* (2021) Effects of artificial light at night on the nest-site selection, reproductive success and behavior of a synanthropic bird. Environmental Pollution, 288, 117805. († equal contributors). https://doi.org/10.1016/j.envpol.2021.117805
  2. Dong, F., Kuo, H.-C., Chen, G.-L., Wu, F., Shan, P.-F., Wang, J., Chen, D., Lei, F.-M., Hung, C.-M.*, Liu, Y.* & Yang, X.-J.* (2021) Population genomic, climatic and anthropogenic evidence suggest the role of human forces in endangerment of green peafowl (Pavo muticus). Proceedings of the Royal Society B, 288, 20210073. https://doi.org/10.1098/rspb.2021.0073
  3. Dong, F.*, Hung, C.-M., Li, S.H.* & Yang X.-J.* (2021) Potential Himalayan community turnover through the Late Pleistocene. Climatic Change, 164, 6. https://doi.org/10.1007/s10584-021-02976-7

2020

  1. Chen, Y.-C., Kuo, H.-C., Lo, W.-S. & Hung, C.-M.* (2020) Avian phenotypic convergence is subject to low genetic constraints based on genomic evidence. BMC Evolutionary Biology, 20, 147. https://doi.org/10.1186/s12862-020-01711-7
  2. Chen, C.-Y., Chen, C.-K., Chen, Y.-Y., Fang, A., Shaw G.T.-W., Hung, C.-M.* & Wang, D.* (2020) Maternal gut microbes shape the early-life assembly of gut microbiota in passerine chicks via nests. Microbiome, 8, 129. https://doi.org/10.1186/s40168-020-00896-9
  3. Dong, F., Hung, C.-M.* & Yang, X.-J.* (2020) Secondary contact after allopatric divergence explains avian speciation and high species diversity in the Himalayan-Hengduan Mountains. Molecular Phylogenetics and Evolution, 143, 106671. https://doi.org/10.1016/j.ympev.2019.106671
  4. Nguyen, H. N., Hung, C.-M., Yang, M.-Y. & Lin, S.-M. (2020). Sympatric competitors have driven the evolution of temporal activity patterns in Cnemaspis geckos in Southeast Asia. Scientific Reports, 10:27. https://doi.org/10.1038/s41598-019-56549-x

2019

  1. Yang, S.-F., Lu, C.-W., Yao, C.-T. & Hung, C.-M.* (2019) To trim, or not to trim: effects of read-trimming on the de novo genome assembly of a widespread East Asian passerine, the rufous-capped babbler (Cyanoderma ruficeps Blyth). Genes, 10, 737. https://doi.org/10.3390/genes10100737
  2. Huang, C.-C., Chen, Y.-Y., Fang, Y.-T., Chen Y.-C. & Hung, C.-M.* (2019) Generating brain matrices for zebra finch brain sectioning using three-dimensional printing technology. Journal of Neuroscience Methods, 327, 108399. https://doi.org/10.1016/j.jneumeth.2019.108399
  3. Lai, Y.T., Yeung, C.K., Omland, K.E., Pang, E.L., Hao, Y., Liao, B.Y., Cao, H.F., Zhang B.W. Yeh, C.F., Hung, C.M., Hung H.Y., Yang, M.Y., Liang W., Hsu, Y.C. Yao, C.T., Dong, L., Lin, K. & Li, S.H.* (2019). Standing genetic variation as the predominant source for adaptation of a songbird. Proceedings of the National Academy of Sciences, 116(6), 2152-2157. https://doi.org/10.1073/pnas.1813597116
  4. Chen, Y.-C., Nazarizadeh, M., Lei, F.-M., Yang, X.-J., Yao, C.-T., Dong, F., Dong, L., Zou, F.-S., Drovetski, S.V., Liu, Y., Huang, C.-C. & Hung, C.-M.* (2019) The niches of nuthatches affect their lineage evolution differently across latitude. Molecular Ecology, 28, 803-817. https://doi.org/10.1111/mec.14980
  5. Nguyen, H.N., Lu, C.-W., Chu, J.-H., Grismer, L.L., Hung, C.-M.* and Lin, S.-M.* (2019) Historical demography of four gecko species specializing in boulder cave habitat –its implications in the evolutionary dead end hypothesis and conservation. Molecular Ecology, 28, 772-784. https://doi.org/10.1111/mec.14985
  6. Wang, J.-S. & Hung, C.-M.* (2019) Barn swallow nest predation by a recent urban invader, the Taiwan whistling thrush – implications for the evolution of urban avian communities. Zoological Studies, 58. 1. https://doi.org/10.6620/ZS.2019.58-01

2018

  1. Hung, C.-M.*, Zink, R.M. & Li, S.-H. (2018) Can genomic variation explain the extinction of the passenger pigeon? Journal of Avian Biology, e01858. https://doi.org/10.1111/jav.01858
  2. Fang, Y.-T., Tuanmu, M.-N.* & Hung, C.-M.* (2018) Asynchronous evolution of interdependent nest characters across the avian phylogeny. Nature Communications, 9, 1863. https://doi.org/10.1038/s41467-018-04265-x
  3. Mays Jr, H.L.*, Hung, C.-M., Shaner, P.-J.L., Denvir, J., Justice, M., Yang, S.-F., Roth, T.L., Oehler, D.A., Fan, J., Rekulapally, D. & Primerano, D.A. (2018) Genomic analysis of demographic history and ecological niche modeling in the endangered Sumatran Rhinoceros Dicerorhinus sumatrensis. Current Biology 28, 70-76. https://doi.org/10.1016/j.cub.2017.11.021

2017

  1. Dong, F.†, Hung, C.-M.†, Li, X.-L., Gao, J.-Y., Zhang, Q., Wu, F., Lei, F.-M.*, Li, S.-H.* & Yang, X.-J.* (2017) Ice age unfrozen: severe effect of the last interglacial, not glacial, climate change on East Asian avifauna. BMC Evolutionary Biology, 17:244. († equal contributors). https://doi.org/10.1186/s12862-017-1100-2
  2. Hung, C.-M.*, Drovetski, S.V. & Zink, R.M. (2017) The roles of ecology, behavior and effective population size in the evolution of a community. Molecular Ecology, 26: 3775-3784. https://doi.org/10.1111/mec.14152

2016

  1. Hung, C.-M., Yu, -Y., Lai, Y.-T. & Shaner, P.-J.L.* (2016) Developing informative microsatellite makers for non-model species using reference mapping against a model species’ genome. Scientific Reports, 6, 23087. https://doi.org/10.1038/srep45419
  2. Hung, C.-M.*, Drovetski, S.V. & Zink, R.M. (2016) Matching loci surveyed to questions asked in phylogeography. Proceedings of the Royal Society B, 283: 20152340. https://doi.org/10.1098/rspb.2015.2340

2014

  1. Hung, C.-M., Hung, H.-Y., Yeh, C.-F., Fu, Y.-Q., Chen, D., Lei, F.-M., Yao, C.-T., Yao, C.-J., Yang, X.-J., Lai, Y.-T. & Li, S.-H.* (2014) Species delimitation in the Chinese bamboo partridge (Bambusicola thoracicus) species complex. Zoologica Scripta, 43, 562-575. https://doi.org/10.1111/zsc.12071
  2. Hung, C.-M. †, Shaner, P.-J.L. †, Zink, R.M., Liu, W.-C., Chu, T.-C., Huang, W.-S.* & Li, S.-H. * (2014) Drastic population fluctuations explain the rapid extinction of the passenger pigeon. Natl. Acad. Sci. U.S.A., 111, 10636-10641. († equal contributors). https://doi.org/10.1073/pnas.1401526111
  3. Hung, C.-M*. & Zink, R.M. (2014) Distinguishing the effects of selection from demographic history in the genetic variation of two sister passerines based on mitochondrial-nuclear comparison. Heredity, 113, 42-51. https://doi.org/10.1038/hdy.2014.9

2013

  1. Hung, C.-M.*, Drovetski, S.V. and Zink, R.M. (2013) Multilocus test of the absence of mtDNA phylogeographic structure in a widespread wader, the common sandpiper (Actitis hypoleucos). Journal of Ornithology, 154, 1105-1113. https://doi.org/10.1007/s10336-013-0980-1
  2. Hung, C.-M., Lin, R.-C., Chu, J.-H., Yeh, C.-F. & Li, S.-H.* (2013) The de novo assembly of mitochondrial genomes of the extinct passenger pigeon (Ectopistes migratorius) with shotgun sequencing. PloS One, e56301. https://doi.org/10.1371/journal.pone.0056301
  3. Hung, C.-M.*, Drovetski, S.V. & Zink, R.M. (2013) Recent allopatric divergence and niche evolution in a widespread Palearctic bird, common rosefinch (Carpodacus erythrinus). Molecular Phylogenetics and Evolution, 66, 103-111. https://doi.org/10.1016/j.ympev.2012.09.012

2012

  1. Hung, C.-M.*, Drovetski, S.V. & Zink, R.M. (2012) Multilocus coalescence analyses support a mtDNA-based phylogeographic history for a widespread Palearctic passerine bird, Sitta europaea. Evolution, 9, 2850-2864. https://doi.org/10.1111/j.1558-5646.2012.01657.x

2004-2011

  1. Hung, C.-M., Li, S.-H. & Lee, L.-L.* (2004) Fecal DNA typing to determine the abundance and spatial organization of otters (Lutra lutra) along two stream systems in Kinmen. Animal Conservation, 7, 301-311. https://doi.org/10.1017/S1367943004001453