Brökeland, W., Wägele, J.W., Bruce, N. (2001): Paravireia holdichi n.sp., an enigmatic isopod crustacean from the Canary Islands with affinities to species from New Zealand. Org. Divers. Evol. 1: 83-98.
Wägele, J.W., Misof, B. (2001): On quality of evidence in phylogeny reconstruction: a reply to Zrzavý’s defence of the „Ecdysozoa“ hypothesis. J. Zool. Syst. Evol. Res. 39: 165-176.
Freyhof, J. & Herder, F. (2001) A new miniature cyprinid from Central Vietnam, Tanichthys micagemmae (Cypriniformes: Cyprinidae). Ichthyological Exploration of Freshwaters 12, 215-220
Jahn, O. (2001): Integrating biological data into development projects: threatened bird species and management plans for sustainable forestry in the Province of Esmeraldas, Ecuador. Pp. 39-53.In Rhoades, R., Stallings, J. (eds.): Integrated Conservation and Development in Tropical America: Experiences and Lessons in Linking Communities, Projects and Policies. SANREM CRSP and CARE – SUBIR, Athens, Georgia, USA.
Fuellen G., Wägele J. W. (2000): Phylogeny inference by minimum conflict. In: Gaul W., Decker R., (eds.) Classification and information processing at the turn of the millenium. Proc. 23rd Ann. Conf. Ges. Klassif., Univ. Bielefeld, vol 2000, pp 377-384.
98) Aydogan, A., Wägele, J.W., Park, J.Y. (2000): New deep-sea isopods (Crustacea, Isopoda, Asellota) from the Atacama-Trench. Mitt. Mus. Nat.kd. Berlin, Zool. Reihe 76: 175-194.
Baltzer, C., Held, C., Wägele, J.W. (2000): Furcarcturus polarsterni n.sp., a large deep sea isopod from the Drake Passage, with a preliminary molecular characterization. Polar Biol.. 23: 833-839.
Diversity and biogeography of Indo-Pacific Calicnemiinae (Odonata: Platycnemididae). Abstracts Biogeography of Southeast Asia 2000 - organisms and orogenesis, June 4-9, 2000, Noordwijkerhout, The Netherlands.
Jahn, O. (2000): Aves amenazadas. Pp. 26-43. In EcoCiencia – Proyecto SUBIR (ed.): Aves del Chocó Ecuatoriano, Diversidad y Tradiciones Orales. EcoCiencia, Quito, Ecuador.
Jahn, O., M.B. Robbins, P. Mena Valenzuela, P. Coopmans, R.S. Ridgely, and K.-L. Schuchmann (2000): Status, ecology and vocalizations of the Five-coloured Barbet Capito quinticolor in Ecuador, with notes on the Orange-fronted Barbet C. squamatus. Bull. B.O.C.120: 16-22. Online at: https://www.biodiversitylibrary.org/page/40025585#page/24/mode/1up
Wägele, J.W. (1999) Homologien, Apomorphien und Grundmuster in der molekularen Systematik (Vergleichende Analyse von DNA-Sequenzen aus phylogenetischer Sicht.) In: Schmitt, M. (ed.) Phylogenetik und Moleküle. Edition Archae, Gelsenkirchen/Schwelm: 83-120.
Schulenburg J.H.G.v.d., Englisch, U., Wägele, J.W: (1999) Evolution of ITS1 rDNA in the Digenea (Platyhelminthes: Trematoda): 3’ end sequence conservation and its phylogenetic utility. J. Mol. Evol. 48: 2-12.
