Systematik und Evolutionsbiologie

Begutachtet

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Data files for the relevant studies can be obtained from TreeBASE or on request.

2017

Bininda-Emonds, O.R.P. and A.-M. Hartmann. 2017. Mammalian evolution: the phylogenetics story. Pp. 77–86 in Evolution of Nervous Systems, 2nd Edition (Kaas, J.H., ed.). Elsevier, Amsterdam.
DownloadGao, Y., D. Wu, L. Wang, C. Lin, C. Ma, X. Xi, M. Zhou, J. D, O.R.P. Bininda-Emonds, T. Chen, and C. Shaw. 2017. Targeted modification of a novel amphibian antimicrobial peptide from Phyllomedusa tarsius to enhance its activity against MRSA and microbial biofilm. Frontiers in Microbiology 8: 628.
DownloadMoore, B.A., L.P. Tyrrell, D. Pita, O.R.P. Bininda-Emonds, and E. Fernández-Juricic. 2017. Does retinal configuration make the head and eyes of foveate birds move? Scientific Reports 7: 38406.
Schimmelpfennig, A., O.R.P. Bininda-Emonds, M. Böer, and U. Gansloßer. 2017. Eingewöhnungs- und Paarbindungsverhalten zweier neuer Sumatratiger (Panthera tigris sumatrae, Pocock 1929) im Osnabrücker Zoo (Acclimatisation and pair formation of two newly introduced Sumatran tigers (Panthera tigris sumatrae, Pocock 1929) in Osnabrück zoo). Der Zoologische Garten 86(1–6): 235–247.
Wilke, T., W.H. Ahlrichs, and O.R.P. Bininda-Emonds. 2017. A comprehensive and integrative re-description of Synchaeta tremula (Müller, 1786) and the newly rediscovered Synchaeta tremuloida Pourriot, 1965. Zootaxa 4276(4):503–518.

2016

DownloadBininda-Emonds, O.R.P., C. Hinz, and W.H. Ahlrichs. 2016. Evidence for the uptake and genomic incorporation of environmental DNA in the “ancient asexual” bdelloid rotifer Philodina roseola. Life 6(3): 38.
DownloadHoppe, N., M. Böer, O.R.P. Bininda-Emonds, and U. Gansloßer. 2016. Über das Raum-Zeit-System von Giraffen (Giraffa camelopardalis, Linnaeus, 1758) im Zoo Osnabrück (The spatio-temporal system of giraffes (Giraffa camelopardalis, Linnaeus, 1758) in the Osnabrück Zoo). Der Zoologische Garten 85(3-4): 131–136.
Riemann, O., W. Ahlrichs, and A. Kieneke. 2016. Marine Meiofauna: Umweltfaktoren, Anpassungen und aktuelle Forschung. Mikroskopie 3(2): 64–85.
DownloadWilms, V., C. Köppl, C. Söffigen, A.-M. Hartmann, and H.G. Nothwang. 2016. Molecular bases of K+ secretory cells in the inner ear: shared and distinct features between birds and mammals. Scientific Reports 6: 34203.

2015

Bininda-Emonds, O.R.P., G.L. Powell, H.A. Jamniczky, A.M. Bauer, and J. Theodor (eds.). 2015. All Animals are Interesting: a Festschrift Celebrating the Career of Anthony P. Russell. BIS Verlag, Oldenburg, Germany. 521 pp.
Hartmann, A.-M., and H.G. Nothwang. 2015. Molecular and evolutionary insights into the structural organization of cation chloride cotransporters. Frontiers in Cellular Neuroscience 8: 470.
Jamniczky, H.A., A.M. Bauer, G.L. Powell, and O.R.P. Bininda-Emonds. 2015. All animals are interesting: an introduction to the volume. Pp. 9–11 in All Animals are Interesting: a Festschrift Celebrating the Career of Anthony P. Russell. (Bininda-Emonds, O.R.P., G.L. Powell, H.A. Jamniczky, A.M. Bauer, and J. Theodor, eds.) BIS Verlag, Oldenburg, Germany.
Kimpel, D., J. Gockel, G. Gerlach, and O.R.P. Bininda-Emonds. 2015. Population structuring in the monogonont rotifer Synchaeta pectinata: high genetic divergence on a small geographical scale. Freshwater Biology 60(7): 1364–1378.    
König, E., O.R.P. Bininda-Emonds, and C. Shaw. 2015. Classification and evolution of anuran skin peptides. Peptides 63(1): 96–117.
Mahadeva, V., Z. Dargaei, E. Ivakine, A.-M. Hartmann, D. Ng, J. Chevrier, J. Ormons, H.G. Nothwang, R. McInnes, and M.A. Woodin, M.A. 2015. Neto2-null mice have impaired GABAergic inhibition and are susceptible to seizures. Frontiers in Neuroscience 9: 368.

2014

DownloadBininda-Emonds, O.R.P. 2014. An introduction to supertree construction (and partitioned phylogenetic analyses) with a view toward the distinction between gene trees and species trees. Pp. 49–76 in Modern Phylogenetic Comparative Methods and their Application in Evolutionary Biology – Concepts and Practice (Garamszegi, L.Z., ed.). Springer, Berlin.
DownloadHartmann, A.-M., D. Tesch, H.-G. Nothwang, and O.R.P. Bininda-Emonds. 2014. Evolution of the cation chloride cotransporter family: ancient origins, gene losses, and subfunctionalization through duplication. Molecular Biology and Evolution 31(2): 434–447.
Download Huang, S., O.R.P. Bininda-Emonds, P.R. Stephens, J.L. Gittleman, and S. Altizer. 2014. Phylogenetically related and ecologically similar carnivores harbor similar parasite assemblages. Journal of Animal Ecology 83(3): 671–680.
Download Raupach, M.J., O.R.P. Bininda-Emonds, T. Knebelsberger, S. Laakmann, J. Pfänder, and F. Leese. 2014. Phylogeographical analysis of Ligia oceanica (Crustacea: Isopoda) reveals two deeply divergent mitochondrial lineages. Biological Journal of the Linnean Society 112(1): 16–30.
DownloadWeber, M., A-M. Hartmann, T. Beyer, A. Ripperger, and H.G. Nothwang. 2014. A novel regulatory locus of phosphorylation in the C-terminus of the potassium chloride cotransporter KCC2 that interferes with N-ethylmaleimide or staurosporine mediated activation. Journal of Biological Chemistry 289(27): 18668–18679.

2013

Download Berry, V., O.R.P. Bininda-Emonds, and C. Semple. 2013. Amalgamating source trees with different taxonomic levels. Systematic Biology 62(2): 231-249.
Bininda-Emonds, O.R.P. 2013. Family Herpestidae - Mongooses. Pp. 293-295 in The Mammals of Africa. Volume V. Carnivores, Pangolins, Equids and Rhinoceroses (Kingdon, J. and M. Hoffmann, eds). Bloomsbury Publishing, London.
Download Ehmann, H., H. Hartwich, C. Salzig, N. Hartmann, M. Clement-Ziza, K. Ushakov, K.B. Avraham, O.R.P. Bininda-Emonds, A.K. Hartmann, P. Lange, E. Friauf and H.G. Nothwang. 2013. Time-dependent gene expression analysis of the developing superior olivary complex. Journal of Biological Chemistry 288(36): 25865-25879.
Download Fischer, C., W.H. Ahlrichs, A.G.J. Buma, W.H. van de Poll, and O.R.P. Bininda-Emonds. 2013. How does the "ancient" asexual Philodina roseola (Rotifera: Bdelloidea) handle potential UVB-induced mutations? The Journal of Experimental Biology 216(16): 3090-3095.

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Fritsch, M., O.R.P. Bininda-Emonds, and S. Richter. 2013. Unraveling the origin of Cladocera by identifying heterochrony in the developmental sequences of Branchiopoda. Frontiers in Zoology 10:35.

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König, E., C. Wesse, A.C. Murphy, M. Zhou, L. Wang, T. Chen, C. Shaw, and O.R.P. Bininda-Emonds. 2013. What is the secret of the Tomato Frog's skin secretion? Molecular cloning of a trypsin inhibitor from Dyscophus guineti (Microhylidae). Organisms Diversity & Evolution 13(3): 453-461.

2012

Download Baker, R.J., O.R.P. Bininda-Emonds, H. Mantilla-Meluk, C.A. Porter, and R.A. Van Den Bussche. 2012. Molecular timescale of diversification of feeding strategy and morphology in New World leaf-nosed bats: a phylogenetic perspective. Pp. 385–409 in Evolutionary History of Bats: Fossils, Molecules and Morphology (Gunnell, G. and N. Simmons, eds). Cambridge University Press, Cambridge.
Download Bininda-Emonds, O.R.P., R.M.D. Beck, and R.D.E. MacPhee. 2012. Rocking clocks and clocking rocks: a critical look at divergence time estimation in mammals. Pp. 38–82 From Clone to Bone: the Synergy of Morphological and Molecular Tools in Paleobiology (Asher, R.J. and J. Müller, eds.). Cambridge University Press, Cambridge.

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Careau, V., O.R.P. Bininda-Emonds, G. Ordonez, and T. Garland, Jr. 2012. Are voluntary wheel running and open-field behavior correlated in mice? Different answers from comparative and artificial selection approaches. Behavior Genetics 42(5): 830–844.

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Fischer C. and W.H. Ahlrichs. 2011 (2012). Revisiting the Cephalodella trophi types. Hydrobiologia 662(1): 205–209.

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König, E., V. Clark, C. Shaw, and O.R.P. Bininda-Emonds. 2012. Molecular cloning of skin peptide precursor-encoding cDNAs from tibial gland secretion of the Giant Monkey Frog, Phyllomedusa bicolor (Anura: Neobatrachia). Peptides 38(12): 371–376.

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König, E., M. Zhou, L. Wang, T. Chen, O.R.P. Bininda-Emonds, and C. Shaw. 2012. Antimicrobial peptides and alytesin are co-secreted from the skin granular glands of the Midwife Toad, Alytes maurus (Alytidae, Anura): possible implications for the evolution of frog skin defensive secretions. Toxicon 60(6); 967–981.

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Moore, B.A., J.M. Kamilar, S.P. Collin, O.R.P. Bininda-Emonds, N.J. Dominy, M.I. Hall, C.P. Heesy, A.N. Iwaniuk, S. Johnsen, T.J. Lisney, E.R. Loew, G. Moritz, S.S. Nava, E. Warrant, K.E. Yopak, and E. Fernández-Juricic. 2012. A novel method for comparative analysis of retinal specialization traits from topographic maps. Journal of Vision 12(12): 13, 1–24.

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Nyakatura, K. and O.R.P. Bininda-Emonds. 2012. Updating the evolutionary history of Carnivora (Mammalia): a new species-level supertree complete with divergence time estimates. BMC Biology 10: 12. (Achieved “Highly accessed” status on BioMed Central)

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Segers, H., W.H. De Smet, C. Fischer, D. Fontaneto, E. Michaloudi, R.L. Wallace, and C.D. Jersabek. 2012. Towards a list of available names in zoology, partim Phylum Rotifera. Zootaxa 3179: 61–68.

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Steinert, G., T. Huelsken, G. Gerlach, and O.R.P. Bininda-Emonds. 2012. Species status and population structure of mussels (Mollusca: Bivalvia: Mytilus spp.) in the Wadden Sea of Lower Saxony (Germany). Organisms Diversity & Evolution 12(4):387–402.

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Wang, Y., O.R.P. Bininda-Emonds, and J.A. Jehle. 2012. Nudivirus genomics and phylogeny. Pp. 33–52 in The Viral Genome: Molecular Structure, Diversity, Gene Expression Mechanisms and Host-Virus Interactions (Garcia, M.L. and V. Romanowski, eds). ISBN 978-953-51-0098-0. InTech.

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Wilts, E.F., D. Wulfken, W.H. Ahlrichs, and P. Martínez Arbizu. 2012. The musculature of Squatinella rostrum (Milne, 1886) (Rotifera: Lepadellidae) as revealed by confocal laser scanning microscopy with additional new data on its trophi and overall morphology. Acta Zoologica 93(1): 14–27.
Download Wilts, E.F., D. Bruns, D. Fontaneto, and W.H. Ahlrichs. 2012. Phylogenetic study on Proales daphnicola Thompson, 1892 (Proalidae) and its relocation to Epiphanes (Rotifera: Epiphanidae). Zoological Anzeiger 251(3): 180–196.

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Wulfken, D. and W.H. Ahlrichs. 2012. The ultrastructure of the mastax of Filinia longiseta (Flosculariaceae, Rotifera): informational value of the trophi structure and mastax musculature. Zoological Anzeiger. 251(4): 270–278.

2011

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Fischer C. and W.H. Ahlrichs. 2011. Revisiting the Cephalodella trophi types. Hydrobiologia 662(1): 205–209.

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Gottschling, M., M. Göker, A. Stamatakis, O.R.P. Bininda-Emonds, I. Nindl, and I.G. Bravo. 2011. Quantifying the phylodynamic forces driving papillomavirus evolution. Molecular Biology and Evolution 28(7): 2101–2113.

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König, E. and O.R.P. Bininda-Emonds. 2011. Evidence for convergent evolution in the antimicrobial peptide system in anuran amphibians. Peptides 32(1): 20–25.

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Rodrigues, A.S.L., R. Grenyer, J.E.M. Baillie, O.R.P. Bininda-Emonds, J.L. Gittleman, M. Hoffmann, K. Safi, J. Schipper, S.N. Stuart, T. Brooks. 2011. Complete, accurate, mammalian phylogenies aid conservation planning, but not much. Philosophical Transactions of the Royal Society of London B: Biological Sciences 366(1578): 2652–2660.

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Wang, Y., O.R.P. Bininda-Emonds, M.M. van Oers, J.M. Vlak, and J.A. Jehle. 2011. The genome of Oryctes rhinoceros nudivirus provides novel insight into the evolution of nuclear arthropod-specific large circular double-stranded DNA viruses. Virus Genes 42(3): 444–456.

2010

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Bininda-Emonds, O.R.P. 2010. The future of supertrees: bridging the gap with supermatrices. Palaeodiversity 3(Suppl.): 99–106.

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Fischer C. and I. Schlupp. 2010. Feeding rates in the sailfin molly Poecilia latipinna and its coexisting sexual parasite, the gynogenetic Poecilia formosa (Poeciliidae, Teleostei). Journal of Fish Biology 77(1): 285–291.
Download Fischer C. and I. Schlupp. 2010. Food selection in the sailfin molly and its coexisting sexual parasite, the gynogenetic Amazon molly. Bulletin of Fish Biology 12(1/2): 65–69.

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Goremykin, V.V. S.V. Nikiforova, and O.R.P. Bininda-Emonds. 2010. Automated removal of noisy data in phylogenomic analyses. Journal of Molecular Evolution 71(5): 319–331.

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Pattengale, N.D., M. Alipour, O.R.P. Bininda-Emonds, B.M.E. Moret, E.J. Gottlieb, and A. Stamatakis. 2010. How many bootstrap replicates are necessary? Journal of Computational Biology 17(3): 337–354.

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Riemann, F. and O. Riemann. 2010. The enigmatic mineral particle accumulations on the cuticular rings of marine desmoscolecoid nematodes – structure and significance explained with clues from live observations. Meiofauna Marina 18: 1–10.

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Riemann, O. and W.H. Ahlrichs. 2010. The evolution of the protonephridial terminal organ across Rotifera with particular emphasis on Dicranophorus forcipatus, Encentrum mucronatum and Erignatha clastopis (Rotifera: Dicranophoridae). Acta Zoologica 91(1): 199–211.
Download Wilts, E.F. and W.H. Ahlrichs. 2010. Proales tillyensis sp.n. (Monogononta: Proalidae), a new rotifer species from North-West Germany, with reconstruction of its somatic musculature. Invertebrate Zoology 7(1): 29–46.
Download Wilts, E.F., P. Martínez Arbizu, and W.H. Ahlrichs. 2010. Description of Bryceella perpusilla n. sp. (Monogononta: Proalidae), a new rotifer species from terrestrial mosses, with notes on the ground plan of Bryceella Remane, 1929. International Journal of Hydrobiology 95(6): 471–481.
Download Wilts, E.F., D. Wulfken, and W.H. Ahlrichs. 2010. Combining confocal laser scanning and transmission electron microscopy for revealing the mastax musculature in Bryceella stylata (Milne, 1886) (Rotifera: Monogononta). Zoologischer Anzeiger 248(4): 285–298.
Download Wulfken, D., E.F. Wilts, P. Martínez Arbizu, and W.H. Ahrlichs. 2010. Comparative analysis of the mastax musculature of the rotifer species Pleurotrocha petromyzon (Notommatidae) and Proales tillyensis (Proalidae) with notes on the virgate mastax type. Zoologischer Anzeiger 249(3–4): 181–194.

2009

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Careau, V., O.R.P. Bininda-Emonds, D. Thomas, M.M. Humphries, and D. Réale. 2009. Exploration strategies map along fast-slow metabolic and life-history continuums in muroid rodents. Functional Ecology 23(1): 150–156.

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Eo, S.H., O.R.P. Bininda-Emonds, and J.P. Carroll. 2009. A phylogenetic supertree of the fowls (Galloanserae, Aves). Zoologica Scripta 38(5): 465–481.

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Fischer C. and I. Schlupp. 2009. Differences in thermal tolerance in coexisting sexual and asexual mollies (Poecilia, Poeciliidae, Teleostei). Journal of Fish Biology 74(7): 1662–1668.

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Fritz, S.A., O.R P. Bininda-Emonds, and A. Purvis. 2009. Geographical variation in predictors of mammalian extinction risk: big is bad, but only in the tropics. Ecology Letters 12(6): 539–549.

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Jones, K.E., J. Bielby, M. Cardillo, S.A. Fritz, J. O'Dell, C.D.L. Orme, K. Safi, W. Sechrest, E.H. Boakes, C. Carbone, C. Connolly, M.J. Cutts, J.K. Foster, R. Grenyer, M. Habib, C.A. Plaster, S.A. Price, E.A. Rigby, J. Rist, A. Teacher, O.R.P. Bininda-Emonds, J.L. Gittleman, G.M. Mace, and A. Purvis. 2009. PanTHERIA: a species-level database of life-history, ecology and geography of extant and recently extinct mammals. Ecology 90(9): 2648. (Supplementary data in Ecological Archives)

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Krumbholz, A., O.R.P. Bininda-Emonds, P. Wutzler, and R. Zell. 2009. Phylogenetics, evolution, and medical importance of polyomaviruses. Infection, Genetics and Evolution 9(5): 784–799.

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Pattengale, N.D., M. Alipour, O.R.P. Bininda-Emonds, B.M.E. Moret, and A. Stamatakis. 2009. How many bootstrap replicates are necessary? Pp. 184–200 in Research in Computational Molecular Biology. 13th Annual International Conference, RECOMB 2009, Tucson, Arizona, USA, May 18–21, 2009, Proceedings (Batzoglou, S., ed.). Lecture Notes in Computer Science: Lecture Notes in Bioinformatics, volume 5541. Springer, Berlin.

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Price, S.A. and O.R.P. Bininda-Emonds. 2009. A comprehensive phylogeny of extant horses, rhinos and tapirs (Perissodactyla) through data combination. Zoosystematics and Evolution 85(2): 277–292.

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Riemann, O., A. Kieneke, and W.H. Ahlrichs. 2009. Phylogeny of Dicranophoridae (Rotifera: Monogononta) – a maximum parsimony analysis based on morphological characters. Journal of Zoological Systematics and Evolutionary Research 47(1): 61–76.

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Riemann, O., E.F. Wilts, W.H. Ahlrichs, and A. Kieneke. 2009. Body musculature of Beauchampiella eudactylota (Gosse, 1886) (Rotifera: Euchlanidae) with additional new data on its trophi and overall morphology. Acta Zoologica 90(3): 265–274.

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Wilts, E.F., O.R.P. Bininda-Emonds, and W.H. Ahlrichs. 2009. Comparison of the predatory rotifers Pleurotrocha petromyzon (Ehrenberg, 1830) and Pleurotrocha sigmoidea Skorikov, 1896 (Rotifera: Monogononta: Notommatidae) based on light and electron microscopic observations. Zootaxa 2130: 1–20.

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Wilts, E.F., W.H. Ahlrichs, and P. Martínez Arbizu. 2009. The somatic musculature of Bryceella stylata (Milne, 1886) (Rotifera: Proalidae) as revealed by confocal laser scanning microscopy with additional new data on its trophi and overall morphology. Zoologischer Anzeiger 248(3): 161–175.

2008

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Bininda-Emonds, O.R.P., M. Cardillo, K.E. Jones, R.D.E. MacPhee, R.M.D. Beck, R. Grenyer, S.A. Price, R.A. Vos, J.L. Gittleman, and A. Purvis. 2008. Corrigendum: The delayed rise of present-day mammals. Nature 456(7219): 274. (Corrected Supplemental Information; main text with differences highlighted)
Download Davies, T.J., S.A. Fritz, R. Grenyer, C.D.L. Orme, J. Bielby, O.R.P. Bininda-Emonds, M. Cardillo, K.E. Jones, J.L. Gittleman, G.M. Mace, and A. Purvis. 2008. Phylogenetic trees and the future of mammalian biodiversity. Proceedings of the National Academy of Sciences of the United States of America 105(Suppl. 1): 11556–11563.
Download Fišer, C., O.R.P. Bininda-Emonds, A. Blejec, and B. Sket. 2008. Can heterochrony help explain the high morphological diversity within the genus Niphargus (Crustacea: Amphipoda)? Organisms Diversity and Evolution 8: 146–162.
Download Kieneke, A., W.H. Ahlrichs, P. Martínez Arbizu, and T. Bartolomaeus. 2008. Ultrastructure of protonephridia in Xenotrichula carolinensis syltensis and Chaetonotus maximus (Chaetonotida, Gastrotricha): comparative evaluation of the gastrotrich excretory organs. Zoomorphology 127: 1–20.
Download Kieneke, A., P. Martínez Arbizu, and O. Riemann. 2008. Anatomy and ultrastructure of the reproductive organs in Dactylopodola typhle (Gastrotricha: Macrodasyida) and their possible functions in sperm transfer. Invertebrate Biology 127: 12–32.
Download  Kieneke, A., P. Martínez Arbizu, and O. Riemann. 2008. Body musculature of Stylochaeta scirtetica Brunson, 1950 and Dasydytes (Setodytes) tongiorgii (Balsamo, 1982) (Gastrotricha: Dasydytidae): a functional approach. Zoologischer Anzeiger 247: 147–158.
Download Kieneke, A. and O. Riemann. 2008. First record of rare dasydytid gastrotrich Setopus tongiorgii (Balsamo, 1982) from central Europe with some biological data. Zootaxa 1680: 59–61.
Download Kieneke, A., Riemann, O., and W.H. Ahlrichs. 2008. Novel implications for the basal internal relationships of Gastrotricha revealed by an analysis of morphological characters. Zoologica Scripta 37: 429–460.
Download Krumbholz, A., O.R.P. Bininda-Emonds, P. Wutzler, and R. Zell. 2008. Evolution of four BK virus subtypes. Infection, Genetics and Evolution 8: 632–643.
Download Riemann, O. and W.H. Ahlrichs. 2008. Ultrastructure and function of the mastax in Dicranophorus forcipatus (Rotifera: Monogononta). Journal of Morphology 269: 698–712.
Download Riemann, O. and A. Kieneke. 2008. First record of males of Encentrum mucronatum Wulfert, 1936 and Encentrum martes Wulfert, 1939 (Rotifera: Dicranophoridae) including notes on males across Rotifera Monogononta. Zootaxa 1701: 63–68.
Download Riemann, O., P. Martínez Arbizu, and A. Kieneke. 2008. Organisation of body musculature in Encentrum mucronatum Wulfert, 1936, Dicranophorus forcipatus (O. F. Müller, 1786) and in the ground pattern of Ploima (Rotifera: Monogononta). Zoologischer Anzeiger 247: 133–145.
Download Welch, J.J., O.R.P. Bininda-Emonds, and L. Bromham. 2008. Correlates of substitution rate variation in mammalian protein-coding sequences. BMC Evolutionary Biology 8:53.

2007

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Beutel, R.G, I. Ribera, and O.R.P. Bininda-Emonds. 2007. A genus-level supertree of Adephaga (Coleoptera).Organisms Diversity and Evolution 7(5): 255–269. (Appendix 2 and Full supertree as TIFF)

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Bielby, J., G.M. Mace, O.R.P. Bininda-Emonds, M. Cardillo, J.L. Gittleman, K.E. Jones, C.D.L. Orme, and A. Purvis. 2007. The fast-slow continuum in mammalian life history: an empirical re-evaluation. The American Naturalist 169(6): 748–757.

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Bininda-Emonds, O.R.P. 2007. Fast genes and slow clades: comparative rates of molecular evolution in mammals. Evolutionary Bioinformatics 2007: 3 59–85.

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Bininda-Emonds, O.R.P., M. Cardillo, K.E. Jones, R.D.E. MacPhee, R.M.D. Beck, R. Grenyer, S.A. Price, R.A. Vos, J.L. Gittleman, and A. Purvis. 2007. The delayed rise of present-day mammals. Nature 446(7135): 507–512. (See 2008 corrigendum above for corrected SI files; News & Views; Podcast) (F1000 evaluation)

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Bininda-Emonds, O.R.P., J.E. Jeffery, M.R. Sánchez-Villagra, J. Hanken, M.W. Colbert, C. Pieau, L. Selwood, C.J. ten Cate, A. Raynaud, C.K. Osabutey, and M.K. Richardson. 2007. Forelimb-hindlimb developmental timing differences across tetrapod phylogeny. BMC Evolutionary Biology 7(182).

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Fritz, U. and O.R.P. Bininda-Emonds. 2007. When genes meet nomenclature: tortoise phylogeny and the shifting generic concepts of Testudo and Geochelone. Zoology 110(4): 298–307. (Erratum)

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Higdon, J.W., O.R.P. Bininda-Emonds, R.M.D. Beck, and S.H. Ferguson. 2007. Phylogeny and divergence of the pinnipeds (Carnivora: Mammalia) assessed using a multigene dataset. BMC Evolutionary Biology 7(216).

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Smirthwaite, J.J., S.D. Rundle, O.R.P. Bininda-Emonds, and J.I. Spicer. 2007. An integrative approach identifies sequence heterochronies in pulmonate snails. Evolution and Development 9(2): 122–130.

2006

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Bininda-Emonds, O.R.P. and A. Stamatakis. 2006. Taxon sampling versus computational complexity and their impact on obtaining the Tree of Life. Pp. 77–95 in Reconstructing the Tree of Life: Taxonomy and Systematics of Species Rich Taxa (Hodkinson, T.R. and J.A.N. Parnell, eds). Systematics Association Special Series, volume 72, CRC Press.

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Beck, R.D.M, O.R.P. Bininda-Emonds, M. Cardillo, F.-G.R. Liu, and A. Purvis. 2006. A higher-level MRP supertree of mammals. BMC Evolutionary Biology 6(93).
Download Fischer, C. and W.H. Ahlrichs. 2006. Cephalodella ungulata n.sp. (Monogononta: Notommatidae), a new rotifer species from North-West Germany, with notes on C. tenuiseta (Burn, 1890). Zootaxa 1378: 49–59.

2005

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Bininda-Emonds, O.R.P. 2005. Supertree construction in the genomic age. Pp. 745–757 in Molecular Evolution: Producing the Biochemical Data, Part B (Zimmer, E. A. and E. Roalson, eds). Methods in Enzymology, volume 395. Elsevier.

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Bininda-Emonds, O.R.P. 2005. transAlign: using amino acids to facilitate the multiple alignment of protein-coding DNA sequences. BMC Bioinformatics 6(156) (June 22, 2005). (Associated benchmark data sets.)

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Bininda-Emonds, O.R.P., R.M.D. Beck, and A. Purvis. 2005. Getting to the roots of matrix representation. Systematic Biology 54(4): 668–672.

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Cardillo, M., G.M. Mace, K.E. Jones, J. Bielby, O.R.P. Bininda-Emonds, W. Sechrest, C.D.L. Orme, and A. Purvis. 2005. Multiple causes of high extinction risk in large mammal species. Science 309(5738): 1239–1241. (Also published in Sciencexpress on July 21, 2005) (Supplemental online material.) (F1000 evaluation)

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Jeffery, J.E., O.R.P. Bininda-Emonds, M.I. Coates, and M.K. Richardson. 2005. A new technique for identifying sequence heterochrony. Systematic Biology 54(2): 230–240.

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Jones, K.E., O.R.P. Bininda-Emonds, and J.L. Gittleman. 2005. Bats, rocks and clocks: diversification patterns in Chiroptera. Evolution 59(10): 2243–2255.

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Price, S.A., O.R.P. Bininda-Emonds, and J.L. Gittleman. 2005. A complete phylogeny of the whales, dolphins and even-toed hoofed mammals (Cetartiodactyla). Biological Reviews 80(3): 445–473. 

2004

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Agapow, P.-M., O.R.P. Bininda-Emonds, K.A. Crandall, J.L. Gittleman, G.M. Mace, J.C. Marshall, and A. Purvis. 2004. The impact of species concept on biodiversity studies. Quarterly Review of Biology 79(2): 161–179.

 

Bininda-Emonds, O.R.P. (ed.) 2004. Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life; Computational Biology, volume 4. Kluwer Academic Publishers, Dordrecht, the Netherlands.

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Bininda-Emonds, O.R.P. 2004. The evolution of supertrees.Trends in Ecology and Evolution 19(6): 315–322.

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Bininda-Emonds, O.R.P. 2004. The phylogenetic position of the giant panda (Ailuropoda melanoleuca): a historical consensus through supertree analysis. Pp. 11–35 in Giant Pandas: Biology and Conservation (Lindburg, D.G. and K. Baragona, eds). University of California Press, Berkeley, CA.

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Published simultaneously in China as Bininda-Emonds, O.R.P. 2003. The phylogenetic position of the giant panda (Ailuropoda melanoleuca): a historical consensus through supertree analysis. Pp. 15–33 in Panda 2000: Conservation Priorities for the New Millennium - Proceedings of an International Conference, San Diego, California, October 15-18, 2000. (Lindburg, D.G. and K. Baragona, eds); Shape of Enrichment, Inc, San Diego, CA.
 

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Bininda-Emonds, O.R.P. 2004. Trees versus characters and the supertree/supermatrix "paradox". Systematic Biology 53(2): 356–359.

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Bininda-Emonds, O.R.P., K.E. Jones, S.A. Price, M. Cardillo, R. Grenyer, and A. Purvis. 2004. Garbage in, garbage out: data issues in supertree construction. Pp. 267–280 in Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life (Bininda-Emonds, O.R.P., ed.); Computational Biology, volume 4. Kluwer Academic Publishers, Dordrecht, the Netherlands.

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Cardillo, M., O.R.P. Bininda-Emonds, E. Boakes, and A. Purvis. 2004. A species-level phylogenetic supertree of marsupials. Journal of Zoology 264(1):11–31.

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Kühn, C., G. Thaller, A. Winter, O.R.P. Bininda-Emonds, B. Kaupe, G. Erhardt, J. Bennewitz, M. Schwerin, and R. Fries. 2004. Evidence for a multiple alleles at the DGAT1 locus better explains a QTL with major effect on milk fat content in cattle. Genetics 167(4): 1873–1881.

2003

  Ahlrichs, W.H. 2003. Rotifera (Rädertiere) und Seison (Teleskophalstiere). Pp. 704–733 in Das Mittelmeer. Fauna, Flora, Ökologie. Band II/1: Bestimmungsführer: Prokaryota, Protista, Fungi, Algae, Plantae, Animalia (bis Nemertea). (Hofrichter, R., ed.) Spektrum Akademischer Verlag, Heidelberg.

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Baryshnikov, G.F., O.R.P. Bininda-Emonds, and A.V. Abramov. 2003. Morphological variability and evolution of the baculum (os penis) in Mustelidae (Carnivora). Journal of Mammalogy 84(2): 673–690.

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Bininda-Emonds, O.R.P. 2003. MRP supertree construction in the consensus setting. Pp. 231–242 in Bioconsensus (Janowitz, M.F., F.-J. Lapointe, F.R. McMorris, B. Mirkin, and F.S. Roberts, eds). DIMACS: Series in Discrete Mathematics and Theoretical Computer Science, volume 61. American Mathematical Society-DIMACS, Providence, Rhode Island.

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Bininda-Emonds, O.R.P. 2003. Novel versus unsupported clades: assessing the qualitative support for clades in MRP supertrees. Systematic Biology 52(6):839–848.

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Bininda-Emonds, O.R.P., J.E. Jeffery, and M.K. Richardson. 2003. Inverting the hourglass: quantitative evidence against the phylotypic stage in vertebrate development. Proceedings of the Royal Society of London B: Biological Sciences 270(1513): 341–346. (Electronic appendices A and B.)

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Bininda-Emonds, O.R.P., J.E. Jeffery, and M.K. Richardson. 2003. Is sequence heterochrony an important evolutionary mechanism in mammals? Journal of Mammalian Evolution 10(4):335–361.

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Bininda-Emonds, O.R.P., K.E. Jones, S.A. Price, R. Grenyer, M. Cardillo, M. Habib, A. Purvis, and J.L. Gittleman. 2003. Supertrees are a necessary not-so-evil: a comment on Gatesy et al. Systematic Biology 52(5): 724–729.

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Stoner, C.J., O.R.P. Bininda-Emonds, and T.M. Caro. 2003. The adaptive significance of coloration in lagomorphs. Biological Journal of the Linnean Society 79(2): 309–328. (Download tree in NEXUS (compressed) format.)

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Winter, A., M. van Eckeveld, O.R.P. Bininda-Emonds, F.A. Habermann, and R. Fries. 2003. Genomic organization of the DGAT2/MOGAT gene family in cattle (Bos taurus) and other mammals. Cytogenetic and Genome Research 102(1-4): 42–47.

2002

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Bininda-Emonds, O.R.P., J.L. Gittleman, and M.A. Steel. 2002. The (super)tree of life: procedures, problems, and prospects. Annual Reviews of Ecology and Systematics 33: 265–289.

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Bininda-Emonds, O.R.P., J.E. Jeffery, M.I. Coates, and M.K. Richardson. 2002. From Haeckel to event-pairing: the evolution of developmental sequences. Theory in Biosciences 121(3): 297–320.

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Jeffery, J.E., O.R.P. Bininda-Emonds, M.I. Coates, and M.K. Richardson. 2002. Analyzing evolutionary patterns in vertebrate embryonic development. Evolution and Development 4(4): 292–302. (Supplementary data)

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Jeffery, J.E., M.K. Richardson M.I. Coates, and O.R.P. Bininda-Emonds. 2002. Analyzing embryonic developmental sequences within a phylogenetic framework. Systematic Biology 51(3): 478–491.

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Jones, K.E, A. Purvis, A. MacLarnon, O.R.P. Bininda-Emonds, and N.B. Simmons. 2002. A phylogenetic supertree of the bats (Mammalia: Chiroptera). Biological Reviews 77(2): 223–259.

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Shapiro, B., D. Sibthorpe, A. Rambaut, J. Austin, G.M. Wragg, O.R.P. Bininda-Emonds, P.L.M. Lee, and A. Cooper. 2002. Flight of the dodo. Science 295(5560): 1683.

2001

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Bininda-Emonds, O.R.P., D.M. Decker-Flum, and J.L. Gittleman. 2001. The utility of chemical signals as phylogenetic characters: an example from the Felidae. Biological Journal of the Linnean Society 72(1): 1–15.

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Bininda-Emonds, O.R.P., J.L. Gittleman, and C.K. Kelly. 2001. Flippers versus feet: comparative trends in aquatic and non-aquatic carnivores. Journal of Animal Ecology 70(3): 386–400.

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Bininda-Emonds, O.R.P. and M.J. Sanderson. 2001. An assessment of the accuracy of MRP supertree construction. Systematic Biology 50(4): 565–579.

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Kanthaswamy, S., O.R.P. Bininda-Emonds, C. Warden, J.L. Viray, and D.G. Smith. 2001. Use of SSR fragment length homozygotes for orangutan systematics. Primates 42(1): 35–45.

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Richardson, M.K., J.E. Jeffery, M.I. Coates, and O.R.P. Bininda-Emonds. 2001. Comparative methods in developmental biology. Zoology 104(3): 278–283.

2000

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Bininda-Emonds, O.R.P. 2000. Factors influencing phylogenetic inference: a case study using the mammalian carnivores. Molecular Phylogenetics and Evolution 16(1): 113–126.

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Bininda-Emonds, O.R.P. 2000. Pinniped brain sizes. Marine Mammal Science 16(2): 469–481.

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Bininda-Emonds, O.R.P., S.G. Brady, M. J. Sanderson, and J. Kim. 2000. Scaling of accuracy in extremely large phylogenetic trees. Pp. 547–558 in Pacific Symposium on Biocomputing 6 (Altman, R.B., A.K. Dunker, L. Hunter, K. Lauderdale, and T.E. Klein, eds). World Scientific Publishing Company, River Edge, New Jersey.

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Bininda-Emonds, O.R.P. and J.L. Gittleman. 2000. Are pinnipeds functionally different from fissiped carnivores? The importance of phylogenetic comparative analyses. Evolution 54(3): 1011–1023.

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Bininda-Emonds, O.R.P., D. Vázquez, and L.L. Manne. 2000. The calculus of biodiversity: integrating phylogeny and conservation. Trends in Ecology and Evolution 15(3): 92–94.

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Crandall, K.A, O.R.P. Bininda-Emonds, G.M. Mace, and R.K. Wayne. 2000. Considering evolutionary processes in conservation biology. Trends in Ecology and Evolution 15(7): 290–295.

1999 and before

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Bininda-Emonds, O.R.P., J.L. Gittleman, and A. Purvis. 1999. Building large trees by combining phylogenetic information: a complete phylogeny of the extant Carnivora (Mammalia). Biological Reviews 74(2): 143–175. (View supertree. Download tree in either NEXUS or CAIC (compressed) formats.)

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Bininda-Emonds, O.R.P. and H.N. Bryant. 1998. Properties of matrix representation with parsimony analyses. Systematic Biology 47(3): 497–508.

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Bininda-Emonds, O.R.P., H.N. Bryant, and A.P. Russell. 1998. Supraspecific taxa as terminals in cladistic analysis: implicit assumptions of monophyly and a comparison of methods. Biological Journal of the Linnean Society 64(1): 101–133.

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Bininda-Emonds, O.R.P. and A.P. Russell. 1996. A morphological perspective on the phylogenetic relationships of the extant phocid seals (Mammalia: Carnivora: Phocidae). Bonner zoologische Monographien 41: 1–256.

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Bininda-Emonds, O.R.P. and A.P. Russell. 1994. Flight style in bats as predicted from wing morphometry: the effects of specimen preservation. Journal of Zoology, London 234(2): 275–287.

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Bininda-Emonds, O.R.P. and A.P. Russell. 1993. Effects of preservation on wing morphometry of the little brown bat (Myotis lucifugus). Journal of Zoology, London 230(1): 141–158.

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Bininda-Emonds, O.R.P. and A.P. Russell. 1992. Minimization of potential problems associated with the morphometry of spirit-preserved bat wings. Collection Forum 8(1): 9–14.