Research work
Biogeography
LEE, H.., LEE, K.-S., HSU, C.H., LEE, C.-W., LI, C.-E., WANG, J.-K., TSENG, C.-C., CHEN, W.-J., et al. (2023) Phylogeny, ancestral ranges and reclassification of sand dollars. Scientific Reports 13, 10199. (link).
LIN, Y.V. HSIAO, W.V., CHEN, W.-J., & DENIS, V. (2022) Habitat change and its consequences on reef fish specialization at biogeographic transition zones. Journal of Biogeography 49(8), 1549-1561 (link).
LIM, H.C., HABIB, A., & CHEN, W.-J. (2021) Comparative Phylogeography and phylogeny of pennah croakers (Teleostei: Sciaenidae) in Southeast Asian waters. Genes 2021; 12(12):1926 (link).
CHEN, W.-J., & BORSA, P. (2020) Diversity, phylogeny, and historical biogeography of large-eye seabreams (Teleostei: Lethrinidae). Molecular Phylogenetics and Evolution 151: 106902 (link).
CAMPBELL, M.A., CHANET, B., CHEN, J.-N. LEE, M.-Y., & CHEN, W.-J. (2019) Origins and relationships of the Pleuronectoidei: Molecular and morphological analysis of living and fossil taxa. Zoologica Scripta 48(5), 640-656 (Link)
LEE, H. , LIN, J.-P. , LI , H.-C., CHANG, L.Y., LEE, K.S., LEE, S.-J., CHEN, W.-J., SANKAR, A., & KANG, S.-C. (2019) Young colonization history of a widespread sand dollar (Echinodermata; Clypeasteroida) in western Taiwan. Quaternary International 528(10), 120-129 (link).
BERTRAND, J.A.M., BORSA, P., & CHEN, W.-J. (2017) Phylogeography of the sergeants Abudefduf sexfasciatus and A. vaigiensis reveals complex introgression patterns between two widespread and sympatric Indo-West Pacific reef fishes. Molecular Ecology 26, 2527–2542 (link).
BORSA, P., DURAND, J.-D., CHEN, W.-J., NICOLAS, H., MUTHS, D., MOU-THAM, G., KULBICKI, M (2016) Comparative phylogeography of the western Indian Ocean reef fauna. Acta Oecologica 72, 72-86 (link).
LO, P.-C., LIU, S.-H., CHAO, N.L., NUNOO, F.K.E, MOK, H.-K. & CHEN, W.-J. (2015) A multi-gene dataset reveals a tropical New World origin and Early Miocene diversification of croakers (Perciformes: Sciaenidae). Molecular Phylogenetics and Evolution 88, 132–143 (link).
LIU, S.-Y.V., CHANG, F.-T., BORSA, P., CHEN, W.-J. & DAI, C.-F. (2014) Phylogeography of the humbug damselfish, Dascyllus aruanus (Linnaeus, 1758): evidence of Indo-Pacific vicariance and genetic differentiation of peripheral populations. Biological Journal of the Linnean Society 113, 931–942 (link).
CHEN, W.-J., LAVOUE, S., BEHEREGARAY, L. B. & MAYDEN, R.L. (2014) Historical biogeography of a new antitropical clade of temperate freshwater fishes. Journal of Biogeography 49, 1806–1818 (link).
CHEN, W.-J., LAVOUE, S, & MAYDEN, R.L. (2013) Evolutionary origin and early biogeography of otophysan fishes (Ostariophysi: Teleostei). Evolution 67, 2218-2239 (link).
LAVOUE, S, MIYA, M., MUSIKASINTHORN, P., CHEN, W.-J., & NISHIDA, M. (2013). Evidence for an Indo-West Pacific Origin of the Clupeoidei (Teleostei: Clupeiformes). PloS One 8, e56485 (link).
LUO, J., YANG, D., SUZUKI, H., WANG, Y., CHEN, W-J., CAMPBELL, K. L. & ZHANG, Y. (2004) Molecular Phylogeny and Biogeography of Oriental Voles: Genus Eothenomys (Muridae, Mammalia). Molecular Phylogenetics and Evolution 33(2): 349-362 (Link) [view PDF].
Biodiversity exploration from the Indo-West Pacific
Shallow water & coral reef associated fauna
CHEN, W.-J., MIkI, R., VEVILL, J., & BORSA, P. (2024) Gymnocranius indicus, a new large-eye seabream from the Indian Ocean. Journal of the Marine Biological Association of the United Kingdom 104, e38, 1-10 (link).
CHEN, W.-J., & BORSA, P. (2020) Diversity, phylogeny, and historical biogeography of large-eye seabreams (Teleostei: Lethrinidae). Molecular Phylogenetics and Evolution 151: 106902 (link).
HURZAID, A., CHAN, T.-Y., NOR MOHD S.A, MUCHLISIN, Z.A., & CHEN, W.-J. (2020) Molecular phylogeny and diversity of penaeid shrimps (Crustacea: Decapoda) from South-East Asian waters. Zoologica Scripta 49(5), 596-613 (link).
DELRIEU‐TROTTIN, E., DURAND, J.‐D., LIMMON, G., SUKMONO, T., KADARUSMAN, SUGEHA, H. Y., CHEN, W.-J., et al. (2020) Biodiversity inventory of the grey mullets (Actinopterygii: Mugilidae) of the Indo‐Australian Archipelago through the iterative use of DNA‐based species delimitation and specimen assignment methods. Evolutionary Applications 13(6), 1451-1467 (link).
FRICKE, R., ALLEN, G.R., AMON, D., ANDREFOUET, S., CHEN, W.-J., KINCH, J., MANA, R., RUSSELL, B.C., TULLY, D., & WHITE, W.T. (2019) Checklist of the marine and estuarine fishes of New Ireland Province, Papua New Guinea, western Pacific Ocean, with 810 new records. Zootaxa4588(1), 1–360 (link).
BAKAR, A.A., ADAMSON, E.A.S., JULIANA, L.H., NOR MOHD S.A., CHEN, W.-J., MAN, A., et al. (2018) DNA barcoding of Malaysian commercial snapper reveals an unrecognized species of the yellow-lined Lutjanus (Pisces:Lutjanidae). PLoS ONE, 13(9): e0202945 (link).
CHEN, W.-J., MIKI, R., & BORSA, P. (2017) Gymnocranius obesus, a new large-eye seabream from the Coral Triangle. Comptes Rendus Biologies 340, 520-530 (link).
LO, P.-C., LIU, S.-H.,. MOHD NOR, S.A. & CHEN, W.-J. (2017) Molecular exploration of hidden diversity in the Indo-West Pacific sciaenid clade. PLoS ONE 12(4): e0176623 (link).
HUNG, K.-W., RUSSELL, B.C., & CHEN, W.-J. (2017) Molecular systematics of threadfin breams and relatives (Teleostei, Nemipteridae). Zoologica Scripta 46, 536-551 (link).
BERTRAND, J.A.M., BORSA, P., & CHEN, W.-J. (2017) Phylogeography of the sergeants Abudefduf sexfasciatus and A. vaigiensis reveals complex introgression patterns between two widespread and sympatric Indo-West Pacific reef fishes. Molecular Ecology 26, 2527–2542 (link).
CHEN, W.-J., HO, H.-C., & BORSA, P. (2016) Taiwanese records of oblong large-eye seabream Gymnocranius oblongus (Teleostei: Lethrinidae) and other rare or undetermined large-eye seabreams. Frontiers in Marine Science 3:107 (link).
BORSA, P., SEMBIRING, A., FAUVELOT, C. & CHEN, W.-J. (2014) Resurrection of Indian Ocean humbug damselfish, Dascyllus abudafur (Forsskal) from synonymy with its Pacific Ocean sibling, Dascyllus aruanus (L.). Comptes Rendus Biologies 337, 709–716 (link).
Deep-sea fauna
TASHIRO, F., & CHEN, W.-J. (2022) Ilyophis singularis (Synaphobranchidae; Ilyophinae), a new deep‐sea eel from the South China Sea. Ichthyological Research. https://doi.org/10.1007/s10228-022-00887-w
LEE, H., PUILLANDRE, N., YASUNORI, K., CHEN, W.-J., & SAMADI, S. (2022) Biodiversity and phylogeny of Cocculinidae (Gastropoda: Cocculinida) in the Indo-West Pacific. Zoological Journal of the Linnean Society, 196(1), 366–392 (link).
HANAFI-PORTIER, M., SAMADI, S., CORBARI, L., CHAN, T.-Y., CHEN, W.-J., CHEN, J.-N., LEE, M.-Y., MAH, C., SAUCEDE, T., BORREMANS, C., & OLU, K. (2021) When imagery and physical sampling work together: towards an integrative methodology of deep-sea image-based megafauna identification. Frontiers in Marine Science 8:749078 (link).
WONG, M.-K., Lee, M.-Y., & CHEN, W.-J. (2021) Integrative taxonomy reveals a rare and new cusk-eel species of Luciobrotula (Teleostei, Ophidiidae) from the Solomon Sea, West Pacific. European Journal Of Taxonomy 750: 52–69 (link).
OKAMOTO, M., CHEN, W.-J., & MOTOMURA, H. (2020) New distributional records of three deepwater cardinalfishes Epigonus angustifrons, E. denticulatus, and E. exodon (Perciformes: Epigonidae) in the South Indian Ocean. Cybium 44(2), 165-168 (link).
OGINO, A., LEE, S.-H., CHEN, W.-J., & MATSUNUMA, M. (2020) Chelidoperca cerasina sp. nov., a new perchlet (Perciformes: Serranidae) from the southwest Pacific Ocean. Ichthyological Research 67, 117-132 (link).
LEE, S.-H., LEE, M.-Y., MATSUNUMA, M., & CHEN, W.-J. (2019) Exploring the phylogeny and species diversity of Chelidoperca (Teleostei: Serranidae) from the western Pacific Ocean by an integrated approach in systematics, with descriptions of three new species and a redescription of C. lecromi Fourmanoir, 1982. Frontiers in Marine Science 6:465 (link).
FRICKE, R., ALLEN, G.R., AMON, D., ANDREFOUET, S., CHEN, W.-J., KINCH, J., MANA, R., RUSSELL, B.C., TULLY, D., & WHITE, W.T. (2019) Checklist of the marine and estuarine fishes of New Ireland Province, Papua New Guinea, western Pacific Ocean, with 810 new records. Zootaxa4588(1), 1–360 (link).
OKAMOTO, M., CHEN, W.-J., & SHINOHARA, G. (2018) Epigonus okamotoi (Perciformes: Epigonidae), a junior synonym of E. draco, with new distributional records for E. atherinoides and E. lifouensis in the West Pacific. Zootaxa 4476 (1): 141–150 (link).
WANG, S.-Y., CHEN, J.-N., RUSSELL, B.C., & CHEN, W.-J. (2018) First record of Gauguin’s blunt-nose lizardfish, Trachinocephalus gauguini Polanco, Acero & Betancur 2016 (Teleostei: Synodontidae) outside the Marquesas Archipelago. Zootaxa 4476 (1): 151–156 (link).
TONGBOONKUA, P., LEE, M.-Y., & CHEN, W.-J., (2018) A new species of sinistral flatfish of the genus Chascanopsetta (Teleostei: Bothidae) from off Papua New Guinea, western Pacific Ocean. Zootaxa 4476 (1): 168–181 (link).
FRICKE, R., CHEN, J.-N., & CHEN, W.-J. (2017) New case of lateral asymmetry in fishes: a new subfamily, genus and species of deep water clingfishes from Papua New Guinea, western Pacific Ocean. Comptes Rendus Biologies 340, 47–62 (link).
CHEN, W.-J., CHEN, J.-N., PERNET, E.-J., & OLU, K.(2016) First record of the coloured righteye flounder, Poecilopsetta colorata(Teleostei: Poecilopsettidae) from the Sakalaves seamounts in the Mozambique Channel. Marine Biodiversity Records 9:83 (link).
HO, H.-C., & CHEN, W.-J. (2013) DNA sequences and morphological variation in Lophiodes iwamotoi Ho, Serét & Shao, 2011 based on new material from New Caledonia. Zootaxa 3682, 594-598 (link).
Marine conservation
KONG, M.-S., HUNG, C.-H., HSU, L.-L., YUAN, H.-W., & CHEN, W.-J. (2023) Exploring genetic diversity and population structure of the Little Tern (Sternula albifrons) in Taiwan based on mtDNA and ddRAD sequencing data. Conservation Genetics (link).
SAMADI, S., PUILLANDRE, P., BOISSELIER, M.-C., CHEN, W.-J., CORBARI, L., MAESTRATI, P., MANA, R., PANTE, E., THUBAUT, J., ZUCCON, D. & HOURDEZ, S. (2015). Patchiness of deep-sea communities in Papua New Guinea and potential susceptibility to anthropogenic disturbances illustrated by seep organisms. Marine Ecology 36 (suppl. 1), 109-132 (link).
Environmental (e)DNA
HSU,T.-H., CHEN, W.-J., & DENIS, V. (2023) Navigating the scales of diversity in subtropical and coastal fish assemblages ascertained by eDNA and visual surveys. Ecological Indicators 148:110044 (link).
Mitochondrial genomics of mollusks and ray-finned fishes
LEE, H., CHEN, W.-J., SAMADI, S., PUILLANDRE, N., TSAI, M-H, AZNAR-CORMAN,L. & SAMADI, S. (2019) Incorporation of deep-sea and small-sized species provides new insights into gastropods phylogeny. Molecular Phylogenetics and Evolution 135, 136–147 (link).
LEE, H., SAMADI, S., PUILLANDRE, N., TSAI, M-H, DAI, C.-F., & CHEN, W.-J. (2016) Eight new mitogenomes for exploring the phylogeny and classification of Vetigastropoda. Journal of Molluscan Studies 82, 534-541 (link).
CAMPBELL, M.A., LOPEZ, J.A, SATOH, T., CHEN, W.-J. & MIYA, M. (2014) Mitochondrial genomic investigation of flatfish monophyly. Gene 551, 176-182 (link).
HE, S., GU, X., MAYDEN, R. L., CHEN, W-J., CONWAY, K. W. & CHEN, Y. (2008) Phylogenetic position of the enigmatic genus Psilorhynchus (Ostariophysi: Cypriniformes): evidence from the mitochondrial genome. Molecular Phylogenetics and Evolution 47(1): 419-425 (Link) [view PDF].
High-level phylogeny of ray-finned fishes of
Elopomorpha
PAREY, E., LOUIS, A., MONTFORT, J., [...], CHEN, W.-J., et al. (2023) Genome structures resolve the early diversification of teleost fishes. Science 379, 572–575 (link).
CHEN, J.-N.,SAMADI, S., & CHEN, W.-J. (2015) Elopomorpha (Teleostei) as a new model fish group for evolutionary biology and comparative genomics. In: Pontarotti, P. (ed.). Evolutionary biology: Biodiversification from genotype to phenotype. Springer Verlag., Switzerland. pp. 329-344 (link).
CHEN, J.-N., J., LOPEZ, J.A., LAVOUE, S., MIYA, M., & CHEN, W.-J. (2014) Phylogeny of the Elopomorpha (Teleostei): evidence from six nuclear and mitochondrial markers. Molecular Phylogenetics and Evolution 70, 152-161 (link).
Clupeocephala
LAVOUÉ, S., BERTRAND, J.A.M., CHEN, W.-J., HO, H.-C., MOTOMURA, H., SADO, T., & MIYA, M. (2017) Phylogenetic position of the rainbow sardine Dussumieria (Dussumieriidae) and its bearing on the early evolution of the Clupeoidei. Gene 623, 41-47 (link).
LAVOUE, S., KONSTANTINIDIS, P., & CHEN, W.-J. (2014) Progress in Clupeiform Systematics. In Biology and Ecology of Anchovies and Sardines (K. Ganias, ed). Science Publishers, Enfield, New Hampshire. pp. 1-42 (link).
CHEN, W.-J., LAVOUE, S, & MAYDEN, R.L. (2013) Evolutionary origin and early biogeography of otophysan fishes (Ostariophysi: Teleostei). Evolution 67, 2218-2239 (link).
Acanthomorpha
CHEN, W.-J., SANTINI, F., CARNEVALE, G., CHEN, J.-N., LIU, S.-H., LAVOUE, S. & MAYDEN, R.L. (2014) New insights on early evolution of spiny-rayed fishes (Teleostei: Acanthomorpha). Frontiers in Marine Science 1, 53 (link).
CHEN, W-J., BONILLO, C. & LECOINTRE, G. (2003) Repeatability of clades as a criterion of reliability: a case study for molecular phylogeny of acanthomorph (teleostei) with larger number of taxa. Molecular Phylogenetics and Evolution 26(2): 262-288 (Link) [view PDF].
CHEN, W-J., ORTÍ, G. & MEYER, A. (2004) Novel evolutionary relationships among four fish model systems. Trends in Genetics 20(9): 424-431 (Link) [view PDF].
Percomorpha
CHEN, W.-J., LAVOUE, S., BEHEREGARAY, L. B. & MAYDEN, R.L. (2014) Historical biogeography of a new antitropical clade of temperate freshwater fishes. Journal of Biogeography 49, 1806–1818 (link).
CAMPBELL, M.A., CHANET, B., CHEN, J.-N. LEE, M.-Y., & CHEN, W.-J. (2019) Origins and relationships of the Pleuronectoidei: Molecular and morphological analysis of living and fossil taxa. Zoologica Scripta 48(5), 640-656 (Link).
CAMPBELL, M.A., CHEN, W.-J., & LOPEZ, J.A. (2014) Molecular data do not provide unambiguous support for the monophyly of flatfishes (Pleuronectiformes): a reply to Betancur-R and Ortí. Molecular Phylogenetics and Evolution 75, 149-153 (link).
CAMPBELL, M.A., CHEN, W.-J., & LOPEZ, J.A. (2013) Are flatfishes (Pleuronectiformes) monophyletic? Molecular Phylogenetics and Evolution 69, 664-673 (link).
CHEN, W-J., RUIZ-CARUS, R. & ORTÍ, G. (2007) Relationships among four genera of mojarras (Teleostei: Perciformes: Gerreidae) from the western Atlantic and their tentative placement among percomorph fishes. Journal of Fish Biology 70 (supplement B): 202-218 (Link).
Cypriniformes tree of Life (CToL) project and the systematics
HIRT, M.V., ARRATIA, G., CHEN, W.-J., MAYDEN, R.L., TANG, K.L., WOOD, R.M., & SIMONS, A.M. (2017) Effects of gene choice, base composition and rate heterogeneity on inference and estimates of divergence times in cypriniform fishes. Biological Journal of the Linnean Society 121, 319-339 (link).
CHANG, C.-H., LI. F. SHAO, K.-T., LIN, Y.-S., MOROSAWA, T. KIM, S., KOO, H. KIM, W., LEE, J.-S., HE, S., SMITH, C., REICHARD, M., MIYA, M., SADO, T., UEHARA, K., LAVOUÉ, S., CHEN, W.-J. & MAYDEN, R.L. (2014) Phylogenetic relationships of Acheilognathidae (Cypriniformes: Cyprinoidea) as revealed from evidence of both nuclear and mitochondrial gene sequence variation: Evidence for necessary taxonomic revision in the family and the identification of cryptic species. Molecular Phylogenetics and Evolution 81, 182-194 (link).
CHEN, W.-J., & MAYDEN, R. L. (2012) Phylogeny of suckers (Teleostei: Cypriniformes: Catostomidae): further evidence of relationships provided by the single-copy nuclear gene IRBP2. Zootaxa 3586, 195-210 (link).
YANG, L., ARUNACHALAM, M., SADO, T., LEVIN, B.A., GOLUBTSOV, A.S., FREYHOF, J., FRIEL, J.P., CHEN, W.-J., HIRT, M.V., MANICKAM, R., AGNEW, M.K., SIMONS, A.M., SAITOH, K., MIYA, M., MAYDEN, R.L. & HE, S. (2012) Molecular phylogeny of the cyprinid tribe Labeonini (Teleostei: Cypriniformes). Molecular Phylogenetics and Evolution 65, 362-379 (link).
TANG, K. L., AGNEW, M. K., CHEN, W.-J., RALEY, M. E., SADO, T., SCHNEIDER, L. M., YANG, L., BART, H. L., HE, S., LIU, H., MIYA, M., SAITOH, K., SIMONS, A. M., WOOD, R. M. & MAYDEN, R. L. (2011) Phylogeny of the gudgeons (Teleostei: Cyprinidae: Gobioninae). Molecular Phylogenetics and Evolution, 61:103-124 (link).
MAYDEN, R. L. & CHEN, W-J. (2010) The world's smallest vertebrate species of the Genus Paedocypris: A new family of freshwater fishes and the sister group to the world's most diverse clade of freshwater fishes (Teleostei: Cypriniformes). Molecular Phylogenetics and Evolution 57:152-175 (Link).
SAITOH, K., CHEN, W-J. & MAYDEN, R.L. (2010) Extensive hybridization and tetrapolyploidy in spined loach fish. Molecular Phylogenetics and Evolution 56(3): 1001-1010 (Link).
CHEN, W-J., LHEKNIM, V. & MAYDEN, R.L. (2009) Molecular phylogeny of the Cobitoidea (Teleostei: Cypriniformes) revisited: Position of enigmatic loach Ellopostoma Vaillant resolved with six nuclear genes. Journal of Fish Biology 75(9): 2197-2208 (Link) [view PDF].
CHEN, W-J. & MAYDEN, R.L. (2009) Molecular systematics of the Cyprinoidea (Teleostei: Cypriniformes), the world's largest clade of freshwater fishes: further evidence from six nuclear genes. Molecular Phylogenetics and Evolution 52(2): 544-549 (Link) [view PDF].
MAYDEN, R.L., CHEN, W-J., BART, H.L., DOOSEY, M.H., SIMONS, A.M., et al. (2009) Reconstructing the phylogenetic relationships of the Earth's most diverse clade of freshwater fishes - order Cypriniformes (Actinopterygii: Ostariophysi): a case study using multiple nuclear loci and the mitochondrial genome. Molecular Phylogenetics and Evolution 51(3): 500-514 (Link) [view PDF] (download supp. material).
CHEN, W-J., MIYA, M., SAITOH, K. & MAYDEN, R.L. (2008) Phylogenetic utility of two existing and four novel nuclear gene loci in reconstructing Tree of Life of ray-finned fishes: The order Cypriniformes (Ostariophysi) as a case study. Gene 423(2): 125-134 (Link) [view PDF] (download supp. data).
SAITOH, K. & CHEN, W-J. (2008) Reducing cloning artifacts for recovery of allelic sequences by T7 endonuclease I cleavage and single re-extension of PCR products - A benchmark. Gene 423(1): 92-95 (Link) [view PDF].
MAYDEN, R.L., TANG, K.L., WOOD, R.M., CHEN, W-J., et al. (2008) Inferring the Tree of Life of the order Cypriniformes, the earth’s most diverse clade of freshwater fishes: implications of varied taxon and character sampling. Journal of Systematics and Evolution 46(3): 424–438 (Link) [view PDF].
CONWAY, K. W., CHEN, W-J. & MAYDEN, R. L. (2008) The 'Celestial Pearl danio' is a miniature Danio (s.s) (Ostariophysi: Cyprinidae): evidence from morphology and molecules. Zootaxa 1686: 1-28 [view PDF] (media).
HE, S., GU, X., MAYDEN, R. L., CHEN, W-J., CONWAY, K. W. & CHEN, Y. (2008) Phylogenetic position of the enigmatic genus Psilorhynchus (Ostariophysi: Cypriniformes): evidence from the mitochondrial genome. Molecular Phylogenetics and Evolution 47(1): 419-425 (Link).
HE, S., MAYDEN, R. L., WANG, X., WANG, W., TANG, K. L., CHEN, W-J. & CHEN, Y. (2008) Molecular phylogenetics of the family Cyprinidae (Actinopterygii: Cypriniformes) as evidenced by sequence variation in the first intron of S7 ribosomal protein-coding gene: further evidence from a nuclear gene of the systematic chaos in the family. Molecular Phylogenetics and Evolution 46(3): 818-829 (Link).
Systematics of the Teleostei with focus on
Flatfishes
CAMPBELL, M.A., CHANET, B., CHEN, J.-N. LEE, M.-Y., & CHEN, W.-J. (2019) Origins and relationships of the Pleuronectoidei: Molecular and morphological analysis of living and fossil taxa. Zoologica Scripta 48(5), 640-656 (Link).
TONGBOONKUA, P., LEE, M.-Y., & CHEN, W.-J., (2018) A new species of sinistral flatfish of the genus Chascanopsetta (Teleostei: Bothidae) from off Papua New Guinea, western Pacific Ocean. Zootaxa 4476 (1): 168–181 (link).
Lethrinidae
CHEN, W.-J., MIkI, R., NEVILL, J., & BORSA, P. (2024) Gymnocranius indicus, a new large-eye seabream from the Indian Ocean. Journal of the Marine Biological Association of the United Kingdom 104, e38, 1-10 (link).
CHEN, W.-J., & BORSA, P. (2020) Diversity, phylogeny, and historical biogeography of large-eye seabreams (Teleostei: Lethrinidae). Molecular Phylogenetics and Evolution 151: 106902 (link).
CHEN, W.-J., MIKI, R., & BORSA, P. (2017) Gymnocranius obesus, a new large-eye seabream from the Coral Triangle. Comptes Rendus Biologies 340, 520-530 (link).
CHEN, W.-J., HO, H.-C., & BORSA, P. (2016) Taiwanese records of oblong large-eye seabream Gymnocranius oblongus (Teleostei: Lethrinidae) and other rare or undetermined large-eye seabreams. Frontiers in Marine Science 3:107 (link).
BORSA, P., HSIAO, D.-R., CARPENTER, K.E., & CHEN, W.-J. (2013) Cranial morphometrics and mitochondrial DNA sequences distinguish cryptic species of the longface emperor (Lethrinus olivaceus), an emblematic fish of Indo-West Pacific coral reefs. Comptes Rendus Biologies 336, 505-514 (link).
BORSA, P., BEAREZ, P., & CHEN, W.-J. (2013) Gymnocranius superciliosus and Gymnocranius satoi, two new large-eye breams (Sparoidea: Lethrinidae) from the Coral Sea and adjacent regions. Comptes Rendus Biologies 336, 233-240 (link).
BORSA, P., COLLET, A., CARASSOU, L., PONTON, D. & CHEN, W-J. (2010) Multiple nuclear and mitochondrial genotyping identifies emperors and large-eye breams (Teleostei: Lethrinidae) from New Caledonia and reveal new large-eye bream species. Biochemical Systematics and Ecology 38: 370-389 (Link).
BORSA, P., BEAREZ, P., & CHEN, W-J. (2010) Gymnocranius oblongus, a new large-eye bream species from New Caledonia (Teleostei: Lethrinidae). Comptes Rendus Biologies 333: 241-247 (Link).
Pomacentridae
BERTRAND, J.A.M., BORSA, P., & CHEN, W.-J. (2017) Phylogeography of the sergeants Abudefduf sexfasciatus and A. vaigiensis reveals complex introgression patterns between two widespread and sympatric Indo-West Pacific reef fishes. Molecular Ecology 26, 2527–2542 (link).
BORSA, P., SEMBIRING, A., FAUVELOT, C. & CHEN, W.-J. (2014) Resurrection of Indian Ocean humbug damselfish, Dascyllus abudafur (Forsskal) from synonymy with its Pacific Ocean sibling, Dascyllus aruanus (L.). Comptes Rendus Biologies 337, 709–716 (link).
LIU, S.-Y.V., CHANG, F.-T., BORSA, P., CHEN, W.-J. & DAI, C.-F. (2014) Phylogeography of the humbug damselfish, Dascyllus aruanus (Linnaeus, 1758): evidence of Indo-Pacific vicariance and genetic differentiation of peripheral populations. Biological Journal of the Linnean Society 113, 931–942 (link).
Deepwater cardinalfishes and clingfishes
OKAMOTO, M., CHEN, W.-J., & MOTOMURA, H. (2020) New distributional records of three deepwater cardinalfishes Epigonus angustifrons, E. denticulatus, and E. exodon (Perciformes: Epigonidae) in the South Indian Ocean. Cybium 44(2), 165-168 (link).
OKAMOTO, M., CHEN, W.-J., & SHINOHARA, G. (2018) Epigonus okamotoi (Perciformes: Epigonidae), a junior synonym of E. draco, with new distributional records for E. atherinoides and E. lifouensis in the West Pacific. Zootaxa 4476 (1): 141–150 (link).
FRICKE, R., CHEN, J.-N., & CHEN, W.-J. (2017) New case of lateral asymmetry in fishes: a new subfamily, genus and species of deep water clingfishes from Papua New Guinea, western Pacific Ocean. Comptes Rendus Biologies 340, 47–62 (link).
Ophidiidae
WONG, M.-K., Lee, M.-Y., & CHEN, W.-J. (2021) Integrative taxonomy reveals a rare and new cusk-eel species of Luciobrotula (Teleostei, Ophidiidae) from the Solomon Sea, West Pacific. European Journal of Taxonomy 750: 52–69 (link).
Lutjanidae
BAKAR, A.A., ADAMSON, E.A.S., JULIANA, L.H., NOR MOHD S.A., CHEN, W.-J., MAN, A., et al. (2018) DNA barcoding of Malaysian commercial snapper reveals an unrecognized species of the yellow-lined Lutjanus (Pisces:Lutjanidae). PLoS ONE, 13(9): e0202945 (link).
Mugilidae
DELRIEU‐TROTTIN, E., DURAND, J.‐D., LIMMON, G., SUKMONO, T., KADARUSMAN, SUGEHA, H. Y., CHEN, W.-J., et al. (2020) Biodiversity inventory of the grey mullets (Actinopterygii: Mugilidae) of the Indo‐Australian Archipelago through the iterative use of DNA‐based species delimitation and specimen assignment methods. Evolutionary Applications 13(6), 1451-1467 (link).
DURAND, J.-D., CHEN, W.-J., SEN, K.-N., ZHANG, C., & BORSA, P. (2012) Genus-level taxonomic changes imposed by the mitochondrial phylogeny of grey mullets (Teleostei: Mugilidae). Comptes Rendus Biologies 335, 687-697 (link).
DURAND, J.-D., SEN, K.-N., CHEN, W.-J., JAMANDRE, B.-W., BLEL, H. DIOP, K., NIRCHIO, M., GARCIA DE LEÓN, J.F., WHITFIELD, A.K., CHANG, C.-W. & BORSA, P. (2012) Systematics of the grey mullets (Teleostei: Mugiliformes: Mugilidae): molecular phylogenetic evidence challenges two centuries of morphology-based taxonomic studies. Molecular Phylogenetics and Evolution 64, 73-92 (link).
Nemipteridae
HUNG, K.-W., RUSSELL, B.C., & CHEN, W.-J. (2017) Molecular systematics of threadfin breams and relatives (Teleostei, Nemipteridae). Zoologica Scripta 46, 536-551 (link).
Sciaenidae
LO, P.-C., LIU, S.-H.,. MOHD NOR, S.A. & CHEN, W.-J. (2017) Molecular exploration of hidden diversity in the Indo-West Pacific sciaenid clade. PLoS ONE 12(4): e0176623 (link).
LO, P.-C., LIU, S.-H., CHAO, N.L., NUNOO, F.K.E, MOK, H.-K. & CHEN, W.-J. (2015) A multi-gene dataset reveals a tropical New World origin and Early Miocene diversification of croakers (Perciformes: Sciaenidae). Molecular Phylogenetics and Evolution 88, 132–143 (link).
Sardines & Anchovies
LAVOUÉ, S., RATMUANGKHWANG, S., HO, H.-C., CHEN, W.-J., SITI AZIZAH, M.N. (2018) Swimbladder evolution of longfin herrings (Pristigasteridae, Teleostei). Zoological Studies 57:39 (link).
LAVOUÉ, S., BERTRAND, J.A.M., Wang, H.-Y., CHEN, W.-J., HO, H.-C., MOTOMURA, H., HATA, H., SADO, T., & MIYA, M. (2017) Molecular systematics of the anchovy genus Encrasicholina in the Northwest Pacific PLoS ONE, 12(7): e0181329 (link).
LAVOUÉ, S., BERTRAND, J.A.M., CHEN, W.-J., HO, H.-C., MOTOMURA, H., SADO, T., & MIYA, M. (2017) Phylogenetic position of the rainbow sardine Dussumieria (Dussumieriidae) and its bearing on the early evolution of the Clupeoidei. Gene 623, 41-47 (link).
LAVOUE, S., KONSTANTINIDIS, P., & CHEN, W.-J. (2014) Progress in Clupeiform Systematics. In Biology and Ecology of Anchovies and Sardines (K. Ganias, ed). Science Publishers, Enfield, New Hampshire. pp. 1-42 (link).
Gerreidae
CHEN, W-J., RUIZ-CARUS, R. & ORTÍ, G. (2007) Relationships among four genera of mojarras (Teleostei: Perciformes: Gerreidae) from the western Atlantic and their tentative placement among percomorph fishes. Journal of Fish Biology 70 (supplement B): 202-218 (Link) [view PDF].
Antarctic notothenioids
DEROME, N., CHEN, W-J., DETTAÏ, A., BONILLO, C. & LECOINTRE, G. (2002) Phylogeny of antarctic dragon fishes (bathydraconidae, notothenioidei, teleostei) and related families based on their anatomy and two mitochondrial genes. Molecular Phylogenetics and Evolution24(1): 139-152 (Link) [view PDF].
CHEN, W-J., BONILLO, C. & LECOINTRE, G. (1998) Phylogeny of the Channichthyidae (Notothenioidei, Teleostei) based on two mitochondrial genes. In: di Prisco, G., Pisano, E. and Clarke, A. (eds.). Fishes of Antarctica. A biological Overview. Springer Verlag. pp. 287-298 [view PDF].
Phylogenomics and evolutionary genomics
PAREY, E., LOUIS, A., MONTFORT, J., [...], CHEN, W.-J., et al. (2023) Genome structures resolve the early diversification of teleost fishes. Science 379, 572–575 (link).
LEE, H., CHEN, W.-J., SAMADI, S., PUILLANDRE, N., TSAI, M-H, AZNAR-CORMAN,L. & SAMADI, S. (2019) Incorporation of deep-sea and small-sized species provides new insights into gastropods phylogeny. Molecular Phylogenetics and Evolution 135, 136–147 (link).
CHEN, J.-N., SAMADI, S., & CHEN, W.-J. (2018) Rhodopsin gene evolution in early teleost fishes. PLoS ONE, 13(11): e0206918 (link).
LEE, H., SAMADI, S., PUILLANDRE, N., TSAI, M-H, DAI, C.-F., & CHEN, W.-J. (2016) Eight new mitogenomes for exploring the phylogeny and classification of Vetigastropoda. Journal of Molluscan Studies 82, 534-541 (link).
CHEN, C.-J., SHIKINA, S., CHEN, W.-J., CHUNG, Y.-J., CHIU, Y.-L., BERTRAND, J.A.M., LEE, Y-.H.,& CHANG, C.-F. (2016) A novel female-specific and sexual reproduction-associated Dmrt gene discovered in the stony coral, Euphyllia ancora. Biology of Reproduction 94(2) 40, 1-13 (link).
CHEN, J.-N.,SAMADI, S., & CHEN, W.-J. (2015) Elopomorpha (Teleostei) as a new model fish group for evolutionary biology and comparative genomics. In: Pontarotti, P. (ed.). Evolutionary biology: Biodiversification from genotype to phenotype. Springer Verlag., Switzerland. pp. 329-344 (link).
SAITOH, K., CHEN, W-J. & MAYDEN, R.L. (2010) Extensive hybridization and tetrapolyploidy in spined loach fish. Molecular Phylogenetics and Evolution 56(3): 1001-1010 (Link).
CHEN, W-J. & MAYDEN, R.L. (2010) A phylogenomic perspective on the new era of ichthyology. BioScience 60(6): 421-432.
CHEN, W-J., ORTÍ, G. & MEYER, A. (2004) Novel evolutionary relationships among four fish model systems. Trends in Genetics 20(9): 424-431 (Link) [view PDF].
Comparative morpho-anatomy of fishes
CAMPBELL, M.A., TONGBOONKUA, P., CHANET, B., & CHEN, W.-J (2020) The distribution of the recessus orbitalis across flatfishes (order: Pleuronectiformes). Journal of Fish Biology 97, 293–297 (link).
CHANET, B., SCHNELL, N. K., GUINTARD, C., & CHEN, W.-J. (2023) Anatomy of the endocrine pancreas in actinopterygian fishes and its phylogenetic implications. Scientific Reports 13, 22501 (link)
Coral research
CHEN, C.-J., CHEN, W.-J., & CHANG, C.-F. (2021) Multispecies spawning of scleractinian corals in nonreefal coral communities of northern Taiwan in the northwestern Pacific Ocean. Bulletin of Marine Science 97(2), 351-371 (link).
BAIRD, A., H., GUEST, J.R., [...], CHEN, W.-J., et al. (2021) The Indo-Pacific coral spawning database. Scientific Data 8, 35 (link).
CHEN, C.-J., CHEN, W.-J., SHIKINA, S., DENIS, V., & CHANG, C.-F. (2020) The plasticity of gonad development of sexual reproduction in a scleractinian coral, Porites lichen. General and Comparative Endocrinology 285:113270 (link).
CHEN, C.-J., SHIKINA, S., CHEN, W.-J., CHUNG, Y.-J., CHIU, Y.-L., BERTRAND, J.A.M., LEE, Y-.H.,& CHANG, C.-F. (2016) A novel female-specific and sexual reproduction-associated Dmrt gene discovered in the stony coral, Euphyllia ancora. Biology of Reproduction 94(2) 40, 1-13 (link).
Bird research
KONG, M.-S., HUNG, C.-H., HSU, L.-L., YUAN, H.-W., & CHEN, W.-J. (2024) Exploring genetic diversity and population structure of the Little Tern (Sternula albifrons) in Taiwan based on mtDNA and ddRAD sequencing data. Conservation Genetics 25, 375–392 (link).
Development of nuclear gene markers for studying phylogenetics, systematics, and evolution of ray-finned fishes
CHEN, W-J., MIYA, M., SAITOH, K. & MAYDEN, R.L. (2008) Phylogenetic utility of two existing and four novel nuclear gene loci in reconstructing Tree of Life of ray-finned fishes: The order Cypriniformes (Ostariophysi) as a case study. Gene 423(2): 125-134 (Link) [view PDF] (download supp. data).
LÓPEZ, J. A., CHEN, W-J. & ORTÍ, G. (2004) Esociform phylogeny. Copeia 2004(3): 449-464 (Link) [view PDF].
CHEN, W-J., BONILLO, C. & LECOINTRE, G. (2003) Repeatability of clades as a criterion of reliability: a case study for molecular phylogeny of acanthomorph (teleostei) with larger number of taxa. Molecular Phylogenetics and Evolution 26(2): 262-288 (Link) [view PDF].
Mechanisms of evolution of fungicide resistance in populations of grapevine downy mildew
CORIO-COSTET, M-F., DUFOUR, M-C., CIGNA, J., ABADIE, P. & CHEN, W-J. (2011) Diversity and fitness of Plasmopara viticola isolates resistant to QoI fungicides. European Journal of Plant Pathology 129:315-329 (link).
CORIO-COSTET, M-F., MARTINEZ, F., DELMOTTE, F., DOUENCE, L., RICHART-CERVERA, S. & CHEN, W-J. (2008) Resistance of Plasmopara viticola to QoIs fungicides: Origin and Diversity. In: Modern fungicides and antifungal compounds V. Dehne, H.W., Deising, H.B., Gisi, U., Kuck, K.H., Russell, P.E. & Lyr, H. (eds). DPG, Braunschweig, Germany, pp. 107-112 .
CHEN, W-J., DELMOTTE, F., RICHARD-CERVERA, S., DOUENCE, L., GREIF, C. & CORIO-COSTET, M-F. (2007) At least two origins of fungicide resistance in grapevine downy mildew populations. Applied and Environmental Microbiology 73: 5162-5172 (Link) [view PDF].
DELMOTTE, F., CHEN, W-J., RICHARD-CERVERA, S., GREIF, C. PAPURA, D., GIRESSE, X., MONDOR-GENSON, G. & CORIO-COSTET, M-F. (2006) Microsatellite DNA markers for Plasmopara viticola, the causal agent of downy mildew of grapes. Molecular Ecology Notes 6(2):379-381 (Link) [view PDF].