Online peer-reviewed journal articles

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This page is intended to store links to free online papers from peer-reviewed journals on evolution-relevant topics. If you come across any, please link to them here under the appropriate heading and provide a brief description.

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Contents 1 Genetics 1.1 Evolution of Hox Genes 2 Dinosaurs and Avian Evolution 2.1 Digital Homology Issues 2.2 Feather Evolution 2.3 Transitional Species 2.4 The Sauriurine/Ornithurine Dichotomy 2.5 Neornithine Evolution 2.6 Theropod Lung Structure and Ventilation 2.7 Odds and Ends 3 General Systematics and Phylogenetics 3.1 Molecular Phylogenetics 3.2 Cladistics 4 Flagellar Evolution 5 Insect Evolution 6 Human Evolution 6.1 Human phylogenetics 6.2 Evolutionary Psychology 6.2.1 Human Mating and Sexual Preferences 6.2.2 Female Menopause 7 Chimpanzee Evolution 8 On Creationism

Genetics

Evolution of Hox Genes

• Minguillon, C. & Garcia-Fernandez, J. 2003. Genesis and evolution of Evx and Mox genes and the extended Hox and ParaHox clusters. Genome Biology, 4: r12. (PDF format) -Pretty self-explanatory.

Dinosaurs and Avian Evolution

Digital Homology Issues

• Burke, A.C. & Feduccia, A. 1997. Developmental patterns and the identification of homologies in the avian hand. Science 278: 666-668. (PDF format) - The authors argue that the digits of non-avian theropods and birds are not homologous.

• Chatterjee, S., Garner, J.P., Thomas, A., Burke, A.C., Feduccia, A., & Hinchliffe, J.R. 1998. Counting the fingers of dinosaurs and birds. Science 280: 355a. -Various short pieces on dinosaur/bird digital homology, mostly critiques of Burke & Feduccia.

• Feduccia, A. 1999. 1,2,3 = 2,3,4: Accommodating the cladogram. Proceedings of the National Academy of Sciences 96: 4740-4742. -One of Feduccia's responses to Gauthier & Wagner (1999), and a general overview of the arguments against the dinosaurian ancestry of birds.

• Gauthier, J.A & Wagner, G.P. 1999. 1,2,3 = 2,3,4: A solution to the problem of the homology of the digits in the avian hand. Proceedings of the National Academy of Sciences 96: 5111-5116. -The authors propose a frame shift to explain the digital homology of birds and non-avian theropods.

• Hinchliffe, J.R. 2002. Developmental basis of limb evolution. International Journal of Developmental Biology 46: 835-845. (PDF format) - Discusses "problems" in limb evolution, including a section on bird digits.

Feather Evolution

• Chuong, C.M. et al. 2000. Evo-devo of feathers and scales: building complex epithelial appendages. Current Opinion in Genetics & Development, 10: 449.456. (PDF format) -A short review of Chuong et al's evo-devo theory of feather evolution, focusing on epithelium-mesenchyme interactions.

• Harris, M.P. et al. 2002. Shh-Bmp2 Signaling Module and the Evolutionary Origin and Diversification of Feathers. Journal of Experimental Zoology 294: 160�176. (PDF format) - Excellent paper on Bmp2 and Shh signaling, and the role that module played in feather evolution.

• Prum, R.O. 1999. Development and evolutionary origin of feathers. Journal of Experimental Zoology 285: 291�306. (PDF format) - Prum's groundbreaking evo-devo theory of feather evolution.

• Prum, R. O. & Brush, A. H. 2002. The evolutionary origin and diversification of feathers. Quaterly Review of Biology 77: 261-295 (PDF format) - Prum & Brush's opus on the new evo-devo model of feather evolution, including a critique of Jones et al. (2000) on the homology of the integumentary appendages of Longisquama insignis. See also Downy Dinos for a discussion of theropod integument and that of Longisquama.

Transitional Species

• Chiappe, L.M. et al. 2001. A new skull of Gobipteryx minuta (Aves: Enantiornithes) from the cretaceous of the Gobi Desert. American Museum Novitates 3346: 1-15. (PDF format) - Skull of enantiornithine Gobipteryx.

• Chiappe, L.M. et al. 2002. New enantiornithines bird from the marine upper Cretaceous of Alabama. Journal of Vertebrate Paleontology 22: 170–174. (PDF format) - Halimornis thompsoni paper.

• Clarke, J.A. & Chiappe, L.M. 2001. A new carinate bird from the late Cretaceous of Patagonia (Argentina). American Museum Novitates 3323: 1-23. (PDF format) - Limenavis patagonica description.

• Clarke, J.A. & Norell M.A. 2002. The morphology and phylogenetic position of Apsaravis ukhaana from the late Cretaceous of Mongolia. American Museum Novitates 3387: 1-46. (PDF format) - Description of the Ornithurine Apsaravis ukhaana. See Discussion of Clarke & Norell (2002) for additional commentary.

• Forster, C.A. et al. 1998. The Theropod Ancestry of Birds: New Evidence from the Late Cretaceous of Madagascar. Science 279: 1915-1919. - Rahona ostromi paper. Note that the generic name of this species was later changed to Rahonavis, which is now the correct rendering.

• Hou, L. et al. 2004. New early Cretaceous fossil from China documents a novel trophic specialization for Mesozoic birds. Naturwissenschaften 91: 22–25. (PDF format) - Enantiornithine Longirostravis hani, with a long, specialized rostrum for feeding. See Discussion of Hou et al. 2004 for additional commentary.

• Hwang, S.H. et al. 2002. New specimens of Microraptor zhaoianus (Theropoda: Dromaeosauridae) from northeastern China. American Museum Novitates, 3381: 1-44. (PDF format) -Long, detailed description of M. zhaoianus.

• Hwang, S.H. et al. 2004. A large compsognathid from the Early Cretaceous Yixian Formation of China. Journal of Systematic Palaeontology 2: 13-30. (PDF format) - Description of new basal compsognathid Huaxiagnathus. The cladistic analysis contains some very interesting conclusions about coelurosaurian phylogeny.

• Ji, Q. et al. 2003. An early ostrich dinosaur and implications for ornithomimosaur phylogeny. American Museum Novitates 3420: 1-19. (PDF format) - Shenzhousaurus description, phylogeny, and biogeography.

• Makovicky, P. et al. 2003. Osteology and relationships of Byronosaurus jaffei (Theropoda: Troodontidae). American Museum Novitates 3402: 1-32. (PDF format) - More detailed look at Byronosaurus.

• Naish, D. & Martill, D.M. 2002. A reappraisal of Thecocoelurus daviesi (Dinosauria: Theropoda) from the early Cretaceous of the Isle of Wight. Proceedings of the Geologists’ Association 113: 23–30. (PDF format) - Argues that Thecocoelurus is actually an oviraptorosaur

• Norell, M. et al. 2000. A new troodontid theropod from Ukhaa Toldog, Mongolia. Journal of Vertebrate Paleontology 20: 7-11. (PDF format) - Original description of Byronosaurus, which lacked dental serrations.

• Xu, X. et al. 1999. A therizinosauroid dinosaur with integumentary structures from China. Nature 399: 350-354. - Original description of feathered therizinosaur Beipiaosaurus inexpectus.

• Xu, X. et al. 2002. A basal troodontid from the early Cretaceous of China. Nature 415: 780-784. (PDF format) - Preliminary description of Sinovenator changii.

• Xu, X. et al. 2002. A ceratopsian dinosaur from China and the early evolution of Cerotopsia. Nature 416: 314-317. (PDF format) - Preliminary description of a basal ceratopsian.

• Xu, X. et al. 2003. Four-winged dinosaurs from China. Nature 421: 335-340. (PDF format) - Microraptor gui paper.

• Zhou, Z. & Zhang, F. 2001. Two new ornithurine birds from the Early Cretaceous of western Liaoning, China. Chinese Science Bulletin 46: 1258-1264. (PDF format) - Description of Yanornis and Yixianornis. See Discussion of Zhou & Zhang (2001) for additional commentary.

The Sauriurine/Ornithurine Dichotomy

• Lianhai Hou, Larry D. Martin, Zhonghe Zhou, Alan Feduccia. 1996. Early adaptive radiation of birds: Evidence from fossils from Northeastern China. Science 274: 1164-1167. An analysis of early ecological diversification and phylogeny of basal birds. The data matrix from this analysis is available at Data Matrix from Hou et al. 1996. Also see Discussion of Hou et al. (1996) for additional commentary on this topic.

Neornithine Evolution

• Benton, M.J. 1999. Early origins of modern birds and mammals: molecules vs. morphology. Bioessays 21: 1043-1051. (PDF format)

• Cooper, A. & Penny. D. Mass survival of birds across the Cretaceous-Tertiary boundary: molecular evidence. Science 275: 1109-1113. (PDF format) - Uses molecular data to argue against "big bang" model of early neornithine evolution.

• Fara, E. & Benton, M.J. 2000. The fossil record of Cretaceous tetrapods. Palaios 15: 161-165. (PDF format) - Argues for an explosive post-KT radiation of both birds and mammals.

• Feduccia, A. 1995. Explosive evolution in Tertiary birds and mammals. Science 267: 637-638. - Feduccia's introductory article on the so-called big bang model of neornithine evolution.

• Feduccia, A. 2003. Big bang for Tertiary birds? Trends in Ecology and Evolution 18: 172-176. (PDF format) - Recent restatement of the case for an explosive post-KT radiation of neornithines.

• Garcia-Moreno, J. & Mindell, D.P. 2000. Rooting a phylogeny with homologous genes on opposite sex chromosomes (gametologs): a case study using avian CHD. Molecular Biology and Evolution 17: 1826-1832. (PDF format) - Molecular study supporting the monophyly of Galloanseres and the basal divergence of paleognaths.

• Garcia-Moreno, J. et al. 2003. Congruent avian phylogenies inferred from mitochondrial and nuclear DNA sequences. Journal of Molecular Evolution 57: 27–37. (PDF format) - Argues for the traditional view of early avian evolution.

• Gussekloo, S.W.S. & Bout, R.G. 2002. Non-neotenous origin of the palaeognathous (Aves) pterygoid–palate complex. Canadian Journal of Zoology 80: 1491–1497. (PDF format) - Presents evidence that the palaeognathous PPC is not neotenous in origin.

• Harlid, A. & Arnason, U. 1999. Analyses of mitochondrial DNA nest ratite birds within the Neognathae: supporting a neotenous origin of ratite morphological characters. Proceedings of the Royal Society of London 266: 305-309. (PDF format). See Discussion of Harlid & Arnason (1999) for further commentary.

• Johansson, U.S. et al. 2001. Clades within the 'higher land birds', evaluated by nuclear DNA sequences. Journal of Zoological Systematics and Evolutionary Research 39: 37-51. (PDF format)

• Johnson, K.P. 2001. Taxon sampling and the phylogenetic position of Passeriformes: evidence from 916 avian cytochrome b sequences. Systematic Biology50: 128-136. (PDF format) - Places Passeriformes basal to other neognaths.

• Mayr, G. 2002. Osteological evidence for paraphyly of the avian order Caprimulgiformes (nightjars and allies). Journal of Ornithology 143: 82-97. (PDF format)

• Mayr, G. et al. 2003. Monophyletic groups within 'higher land birds' - comparison of morphological and molecular data. Journal of Zoological Systematics and Evolutionary Research 41: 223-248. (PDF format)

• Mindell, D.P. et al. 1999. Interordinal relationships of birds and other reptiles based on whole mitochondrial genomes. Systematic Biology 48: 138–152. (PDF format) - Finds Passeriformes to be the most basal crown lineage, with ratites as the sister clade to Galloanseres.

• van Tuinen, M. et al. 2000. The early history of modern birds inferred from DNA sequences of nuclear and mitochondrial ribosomal genes. Molecular Biology and Evolution 17: 451–457. (PDF format) - Molecular support for neognath holophyly and a traditional view of neornithine evolution, with Passeriformes occupying a derived position.

• van Tuinen, M. et al. 2003. ‘Big bang’ for Tertiary birds? a reply. Trends in Ecology and Evolution 18: 442-443. (PDF format) - A reply to Alan Feduccia's views on neornithine origins, and a response by Feduccia. See The Neornithine 'Big Bang' for additional discussion.

• van Tuinen, M. & Hedges, S.B. 2004. The effect of external and internal fossil calibrations of the avian evolutionary timescale. Journal of Paleontology 78: 45-50. (PDF format)

Theropod Lung Structure and Ventilation

• Ruben, J.A. et al. 1997. Lung structure and ventilation in theropod dinosaurs and early birds. Science 278: 1267-1247. - Argues that theropods possesed a pelvovisceral pump. For a critique, see A Reply to Ruben on Theropod Physiology.

• Ruben, J.A. et al. 2003. Respiratory and reproductive paleophysiology of dinosaurs and early birds. Physiological and Biochemical Zoology 76: 141–164. (PDF format) - The latest from Ruben, Jones and Geist. For a critique see A Reply to Ruben on Theropod Physiology.

Odds and Ends

• Feduccia, A. 2002. Birds are dinosaurs: Simple answer to a complex problem. The Auk 119(4): 1187-1201. - The latest work from Alan Feduccia, reviewing the current status of opposition to the theropod origin of birds. Includes his endorsement of MANIAC.

• Hedges, S.B. 1994. Molecular evidence for the origin of birds. Proceedings of the National Academy of Sciences, 91: 2621-2624. (PDF format) -Molecular techniques establish that crocs are the living group most closely related to birds. See Discussion of Hedges (1994).

• Holtz, T.R. 1998. A new phylogeny of the carnivorous dinosaurs. Gaia 15: 5-61. (PDF format) - Holtz's phylogeny of Theropoda.

• Maryanska, T. et al. 2002. Avialan status for Oviraptorosauria. Acta Palaeontologica Polonica 47: 97-116. (PDF format) - The authors find that Oviraptorosauria is an avian clade most closely related to Confuciusornis. See Discussion of Maryanska et al. (2002) for additional commentary.

• Padian, K. & L.M. Chiappe. 1998. The origin and early evolution of birds. Biological Reviews 73: 1-42. (PDF format) - Great, if somewhat dated, review of issues surrounding bird origins.

• Pisani, D. et al. 2002. A genus-level supertree of the Dinosauria. Proceedings of the Royal Society of London B 268: 915-921. (PDF format) - Massive phylogeny of Dinosauria.

• Prum, R.O. 2003. Dinosaurs take to the air. Nature 421: 323-324. (PDF format) - Prum's take on what Microraptor gui means for the theropod origin of birds and feather evolution.

• Sereno, P.C. 1999. The evolution of dinosaurs. Science 284: 2137-2147. (PDF format) - One of the most exhaustively thorough phylogenetic analyses of Dinosauria undertaken, though several of its conclusions are contentious. Sereno's enormous character data and matrices are available here. See Discussion of Sereno (1999) for additional commentary.

• Suzuki, S. et al. 2002. A new specimen of Shuvuuia deserti Chiappe et al., 1998 from the Mongolian late Cretaceous with a discussion of the relationships of alvarezsaurids to other theropod dinosaurs. Contributions in Science 494: 1-18. (PDF format) - Discussion of Shuvuuia, and critique of the characters Sereno (1999 above) used to support the relationship of alvarezsaurids to ornithomimosaurs.

General Systematics and Phylogenetics

Molecular Phylogenetics

• Penny, D. & Hendy, M.D. 1986. Estimating the reliability of phylogenetic trees. Molecular Biology and Evolution, 3: 403-417. (PDF format) -The authors estimate the reliability of phylogenetic trees using protein sequences from 11 taxa.

• Rannala, B. & Yang, Z. 1996. Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. Journal of Molecular Evolution, 43: 304-311. (PDF format) -Description of a new molecular phylogenetic technique.

Cladistics

• Benton, M.J. 2000. Stems, nodes, crown clades, and rank-free lists: is Linnaeus dead? Biological Reviews 75: 633-648. -A critical look at phylogenetic nomenclature.

• Brower, A. 1999. Evolution is not a necessary assumption of cladistics. Cladistics 16: 143-154. (PDF format) - Reviews the history of, and methodology behind cladistics, as well as argues what the title implies.

• Lee, M.S.Y. 2002. Divergent evolution, hierarchy and cladistics. Zoologica Scripta 31:217-219. (PDF format) - A somewhat critical look at a few of the assumptions behind cladistics.

• Lyons-Weiler, J. et al. 1996. Relative apparent synapomorphy analysis (RASA) I: the statistical measurment of phylogenetic signal. Molecular Biology and Evolution 13: 749-757. (PDF format) -What RASA is, and how it works.

• Rae, T.C. 1998. The logical basis for the use of continuous characters in phylogenetic systematics. Cladistics 14: 221-228. (PDF format) - Favorable look at the use of continuous characters in cladistic analyses.

Flagellar Evolution

• Gophna, U. et al. 2003. Bacterial type III secretion systems are ancient and evolved by multiple horizontal-transfer events. Gene 312: 151-163. -- Argues that the TTSS and flagellar export mechanisms share common ancestry.

Insect Evolution

• Branham, M.A. & Wenzel, J.W. 2002. The origin of photic behavior and the evolution of sexual communication in fireflies (Coleoptera: Lampyridae). Cladistics 19: 1-22. (PDF format) - Lots of interesting stuff about firefly evolution.

• Ogden,T.H. & Whiting, M.F. 2003. The problem with "the Paleoptera Problem:" sense and sensitivity. Cladistics 19: 432-442. (PDF format) - On the phylogeny of winged insects.

Human Evolution

Human phylogenetics

• Duarte, C. et al. 1999. The early upper Paleolithic human skeleton from the Abrigo do Lagar Velho (Portugal) and modern human emergence in Iberia. Proceedings of the National Academy of Sciences, 96: 7604-7609. -A description of a child which the authors believe is a neanderthal-sapien hybird.

• Griffiths, D.J. 2001. Endogenous retroviruses in the human genome sequence. Genome Biology, 2: 1017.1-1017.5.

• Ingman, M. et al. 2000. Mitochondrial genome variation and the origin of modern humans. Nature 408: 708-713. (PDF format) - Provides mtDNA evidence for Out of Africa

• Johnson, W.E. & Coffin, J.M. 1999. Constructing primate phylogenies from ancient retrovirus sequences. Proceedings of the National Academy of Sciences, 96: 10254-10260.

• Tattersall, I. & Schwartz, J.H. 1999. Hominids and hybrids: the place of Neanderthals in human evolution. Proceedings of the National Academy of Sciences, 96: 7117-7119. -The authors critique the interpretation of the Lagar Velho child by Duarte et al (1999).

• Wood, B. & Richmond, B.G. 2000. Human evolution: taxonomy and paleobiology. Journal of Anatomy 196: 19-60. (PDF format) - A long, detailed review of human evolution and transitional species.

Evolutionary Psychology

Human Mating and Sexual Preferences

• Freese, J. & Meland, S. 2002. Seven tenths incorrect: heterogeneity and change in the waist-to-hip ratios of Playboy centerfold models and Miss America pageant winners. Journal of Sex Research, May 2002. -A critique of Waist-Hip Ratio research done by Sighn (1993).

• Furnham, A. et al. 1998. The role of body weight, waist-to-hip ratio, and breast size in judgements of female attractiveness. Sex Roles: A Journal of Research, Aug 1998. -An overview of research on the topics in the title. Includes a new study on breast size preferences.

Female Menopause

• Hawkes, K. et al. 1998. Grandmothering, menopause, and the evolution of human life histories. Proceedings of the National Academy of Sciences 95: 1336-1339. (PDF format) - Attempts to explain menopause in terms of grandmothering behavior.

Chimpanzee Evolution

• Whiten, A. et al. 1999. Cultures in chimpanzees. Nature 399: 682-685. (PDF format) - Chimps have evolved the capacity for culture too.

On Creationism

• Pennock, R.T. 2003. Creationism and intelligent design. Annual Review of Genomics and Human Genetics 4: 143-163. (PDF format)