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Systematics and Evolutionary Biology

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

2008 and "in press"

	Bininda-Emonds, O.R.P. In press. Herpestidae. Accepted by The Mammals of Africa. Volume 5. Carnivora, Pholidota, Perissodactyla (Kingdon, J., T. Butynski, and D. Happold) on November 23, 2005. Academic Press, Amsterdam.
	Careau, V., O.R.P. Bininda-Emonds, D. Thomas, M.M. Humphries, and D. Réale. In press. Exploration strategies map along fast-slow metabolic and life-history continuums in muroid rodents. Accepted by Functional Ecology on July 17, 2008.
	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)
	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.
	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.
	Kieneke, A., Martínez Arbizu, P., O. and 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.
	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.
	Kieneke, A., Riemann, O., W.H. and Ahlrichs. 2008. Novel implications for the basal internal relationships of Gastrotricha revealed by an analysis of morphological characters. Zoologica Scripta 37: 429–460.
	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.
	Riemann, O. and W.H. Ahlrichs. 2008. Ultrastructure and function of the mastax in Dicranophorus forcipatus (Rotifera: Monogononta). Journal of Morphology 269: 698–712.
	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.
	Riemann, O., Kieneke, A., and W.H. Ahlrichs. In press. Phylogeny of Dicranophoriadae (Rotifera: Monogononta) – a maximum parsimony analysis based on morphological characters. Accepted by Journal of Zoological Systematics and Evolutionary Research on April 30, 2008.
	Riemann, O., Martínez Arbizu, P., 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.
	Riemann, O., E.F. Wilts, W.H. Ahlrichs, and A. Kieneke. In press. Body musculature of Beauchampiella eudactylota (Gosse, 1886) (Rotifera: Euchlanidae) with additional new data on its trophi and overall morphology. Accepted by Acta Zoologica on June 16, 2008.
	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

	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)
	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.
	Bininda-Emonds, O.R.P. 2007. Fast genes and slow clades: comparative rates of molecular evolution in mammals. Evolutionary Bioinformatics 2007: 3 59–85.
	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 corrigendum for corrected SI files; News & Views; Podcast) (F1000 evaluation)
	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).
	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)
	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).
	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

	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. (Note: The PDF is of a page proof. As such, the page numbers are wrong and the text contains some minor mistakes.)
	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).
	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

	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.
	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.)
	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.
	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)
	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.
	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.
	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

	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.
	Bininda-Emonds, O.R.P. 2004. The evolution of supertrees.Trends in Ecology and Evolution 19(6): 315–322.
	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.
	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.
	Bininda-Emonds, O.R.P. 2004. Trees versus characters and the supertree/supermatrix "paradox". Systematic Biology 53(2): 356–359.
	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.
	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.
	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.
	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.
	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.
	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.
	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.)
	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.
	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.
	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. (View supertree. Download tree in NEXUS (compressed) format.)
	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

	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.
	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.
	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.
	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.
	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.
	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

	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.
	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.
	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.
	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.
	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

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

	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.)
	Bininda-Emonds, O.R.P. and H.N. Bryant. 1998. Properties of matrix representation with parsimony analyses. Systematic Biology 47(3): 497–508.
	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.
(NB: 85 MB)	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.
	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.
	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.
	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.

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