@article{clarke_ksepka_smith_norell_2014, title={Combined phylogenetic analysis of a new North American fossil species confirms widespread Eocene distribution for stem rollers (vol 157, pg 586, 2009)}, volume={172}, number={1}, journal={Zoological Journal of the Linnean Society}, author={Clarke, J. A. and Ksepka, D. T. and Smith, N. A. and Norell, M. A.}, year={2014}, pages={226–229} }
 @article{ksepka_clarke_2012, title={A new stem parrot from the Green River formation and the complex evolution of the grasping foot in Pan-Psittaciformes}, volume={32}, number={2}, journal={Journal of Vertebrate Paleontology}, author={Ksepka, D. T. and Clarke, J. A.}, year={2012}, pages={395–406} }
 @article{boyd_cleland_marrero_clarke_2011, title={Exploring the effects of phylogenetic uncertainty and consensus trees on stratigraphic consistency scores: A new program and a standardized method}, volume={27}, number={1}, journal={Cladistics}, author={Boyd, C. A. and Cleland, T. P. and Marrero, N. L. and Clarke, J. A.}, year={2011}, pages={52–60} }
 @article{eddy_clarke_2011, title={New information on the cranial anatomy of Acrocanthosaurus atokensis and its implications for the phylogeny of Allosauroidea (Dinosauria: Theropoda)}, volume={6}, number={3}, journal={PLoS One}, author={Eddy, D. R. and Clarke, J. A.}, year={2011} }
 @article{nesbitt_ksepka_clarke_2011, title={Podargiform affinities of the enigmatic Fluvioviridavis platyrhamphus and the early diversification of strisores ("caprimulgiformes" plus apodiformes)}, volume={6}, number={11}, journal={PLoS One}, author={Nesbitt, S. J. and Ksepka, D. T. and Clarke, J. A.}, year={2011} }
 @article{clarke_ksepka_salas-gismondi_altamirano_shawkey_d'alba_vinther_devries_baby_2010, title={Fossil evidence for evolution of the shape and color of penguin feathers}, volume={330}, number={6006}, journal={Science}, author={Clarke, J. A. and Ksepka, D. T. and Salas-Gismondi, R. and Altamirano, A. J. and Shawkey, M. D. and D'Alba, L. and Vinther, J. and DeVries, T. J. and Baby, P.}, year={2010}, pages={954–957} }
 @article{ksepka_clarke_2010, title={Primobucco mcgrewi (Aves: Coracii) from the Eocene Green River Formation: Mew anatomical data from the earliest constrained record of stem rollers}, volume={30}, number={1}, journal={Journal of Vertebrate Paleontology}, author={Ksepka, D. T. and Clarke, J. A.}, year={2010}, pages={215–225} }
 @article{ksepka_clarke_2009, title={AFFINITIES OF PALAEOSPIZA BELLA AND THE PHYLOGENY AND BIOGEOGRAPHY OF MOUSEBIRDS (COLIIFORMES)}, volume={126}, ISSN={["1938-4254"]}, DOI={10.1525/auk.2009.07178}, abstractNote={ABSTRACT. Palaeospiza bella was described as an oscine songbird in the late 19th century. The late Eocene age of the holotype specimen would make it the oldest Northern Hemisphere record of the Passeriformes. However, few recent workers have accepted the placement of P. bella within Passeriformes, and the higher relationships of this fossil have remained controversial. We show that P. bella is a member of the Coliiformes (mousebirds) and represents the latest North American occurrence of a clade with an exclusively African extant distribution. Coliiformes are now known from the latest Paleocene to the approach of the Eocene-Oligocene boundary in North America. We present a redescription of P. bella and a new phylogenetic analysis of fossil and living Coliiformes based on a matrix including 49 characters and 18 ingroup taxa. The results of this analysis place P. bella in Colii, the clade comprising taxa more closely related to Coliidae (crown mousebirds) than to the extinct Sandcoleidae. The oldest stem-group Coliiformes are late Paleocene (about 56.2–56.6 Ma) in age. However, no fossil taxon can be confidently placed within the crown clade Coliidae at present. Phylogenetic results imply that a minimum of three mousebird dispersals from Europe to North America occurred during the Early Cenozoic. Review of the early Eocene fossil Eocolius walkeri from the London Clay shows that this taxon lacks convincing coliiform synapomorphies and should be removed from the clade.}, number={2}, journal={AUK}, author={Ksepka, Daniel T. and Clarke, Julia A.}, year={2009}, month={Apr}, pages={245–259} }
 @article{clarke_ksepka_smith_norell_2009, title={Combined phylogenetic analysis of a new North American fossil species confirms widespread Eocene distribution for stem rollers (Aves, Coracii)}, volume={157}, ISSN={["1096-3642"]}, DOI={10.1111/j.1096-3642.2009.00550.x}, abstractNote={We report a nearly complete skeleton of a new species of stem roller (Aves, Coracii) from the early Eocene Green River Formation of North America. The new species is most closely related to two species-depauperate lineages, Coraciidae (rollers) and Brachypteraciidae (ground rollers), that form a monophyletic crown clade (Coracioidea) with an exclusively Old World extant distribution. Phylogenetic analysis utilizing a matrix of 133 morphological characters and sequence data from three genes (RAG-1, c-myc, and ND2) identifies the new species as a stem member of the Coracii more closely related to the crown clade than the only previously identified New World taxon, Primobucco mcgrewi. The phylogenetic placement of the new species and Primobucco mcgrewi indicates a widespread northern hemisphere distribution in the Eocene with subsequent restriction to Africa, Madagascar, Australia, and temperate to tropical parts of Europe and Asia. It provides evidence of further ecological diversity in early stem Coracii and convergence on crown morphologies. The new species contributes to mounting evidence that extant distributions for major avian subclades may be of comparatively recent origin. Further late Palaeogene sampling is needed to elucidate potential drivers for shifting avian distributions and disappearance of Coracii from North America.}, number={3}, journal={ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY}, author={Clarke, Julia A. and Ksepka, Daniel T. and Smith, N. Adam and Norell, Mark A.}, year={2009}, month={Nov}, pages={586–611} }
 @article{boyd_brown_scheetz_clarke_2009, title={TAXONOMIC REVISON OF THE BASAL NEORNITHISCHIAN TAXA THESCELOSAURUS AND BUGENASAURA}, volume={29}, ISSN={["1937-2809"]}, DOI={10.1671/039.029.0328}, abstractNote={ABSTRACT Considerable controversy surrounds the taxonomy and phylogenetic relationships of Maastrichtian basal neornithischian taxa from North America. Discovery of previously unrecognized cranial material from the paratype specimen of Thescelosaurus neglectus (USNM 7758), along with the examination of two new specimens that preserve nearly complete skulls and mandibles, allows for reevaluation of specimens previously referred to Thescelosaurus that preserve cranial material, including the holotypes of Bugenasaura infernalis (SDSM 7210) and Parksosaurus warreni (ROM 804). A phylogenetic analysis was conducted that included as terminals the holotypes of B. infernalis and P. warreni, the type series of T. neglectus, and six specimens previously referred to Thescelosaurus. This analysis is the first to recover a clade containing all basal neornithischian taxa from the Cretaceous of North America, within which P. warreni is recovered as the sister taxon to a Thescelosaurus clade whose monophyly is supported by five cranial autapomorphies. The results of this analysis support: (1) the synonymization of Bugenasaura with Thescelosaurus; (2) the removal of ROM 804 from Thescelosaurus; and (3) the validity of Thescelosaurus garbanii and its referral to Thescelosaurus despite its fragmentary nature. Currently, Parksosaurus and Thescelosaurus are the only basal neornithischian taxa definitively known from Maastrichtian age sediments of North America, while other basal neornithischian taxa proposed to demonstrate fossorial behavior (i.e., Orodromeus, Oryctodromeus, and Zephyrosaurus) are known from Campanian and older sediments. This temporal segregation may support previous hypotheses of an environmental or ecological shift during the latest Cretaceous in North America.}, number={3}, journal={JOURNAL OF VERTEBRATE PALEONTOLOGY}, author={Boyd, Clint A. and Brown, Caleb Marshall and Scheetz, Rodney D. and Clarke, Julia A.}, year={2009}, month={Sep}, pages={758–770} }
 @article{zhou_clarke_zhang_2008, title={Insight into diversity, body size and morphological evolution from the largest Early Cretaceous enantiornithine bird}, volume={212}, ISSN={["1469-7580"]}, DOI={10.1111/j.1469-7580.2008.00880.x}, abstractNote={Abstract}, number={5}, journal={JOURNAL OF ANATOMY}, author={Zhou, Zhonghe and Clarke, Julia and Zhang, Fucheng}, year={2008}, month={May}, pages={565–577} }
 @article{clarke_middleton_2008, title={Mosaicism, modules, and the evolution of birds: Results from a Bayesian approach to the study of morphological evolution using discrete character data}, volume={57}, ISSN={["1076-836X"]}, DOI={10.1080/10635150802022231}, abstractNote={The study of morphological evolution after the inferred origin of active flight homologous with that in Aves has historically been characterized by an emphasis on anatomically disjunct, mosaic patterns of change. Relatively few prior studies have used discrete morphological character data in a phylogenetic context to quantitatively investigate morphological evolution or mosaic evolution in particular. One such previously employed method, which used summed unambiguously optimized synapomorphies, has been the basis for proposing disassociated and sequential "modernizing" or "fine-tuning" of pectoral and then pelvic locomotor systems after the origin of flight ("pectoral early-pelvic late" hypothesis). We use one of the most inclusive phylogenetic data sets of basal birds to investigate properties of this method and to consider the application of a Bayesian phylogenetic approach. Bayes factor and statistical comparisons of branch length estimates were used to evaluate support for a mosaic pattern of character change and the specific pectoral early-pelvic late hypothesis. Partitions were defined a priori based on anatomical subregion (e.g., pelvic, pectoral) and were based on those hypothesized using the summed synapomorphy approach. We compare 80 models all implementing the M(k) model for morphological data but varying in the number of anatomical subregion partitions, the models for among-partition rate variation and among-character rate variation, as well as the branch length prior. Statistical analysis reveals that partitioning data by anatomical subregion, independently estimating branch lengths for partitioned data, and use of shared or per partition gamma-shaped among-character rate distribution significantly increases estimated model likelihoods. Simulation studies reveal that partitioned models where characters are randomly assigned perform significantly worse than both the observed model and the single-partition equal-rate model, suggesting that only partitioning by anatomical subregion increases model performance. The preference for models with partitions defined a priori by anatomical subregion is consistent with a disjunctive pattern of character change for the data set investigated and may have implications for parameterization of Bayesian analyses of morphological data more generally. Statistical tests of differences in estimated branch lengths from the pectoral and pelvic partitions do not support the specific pectoral early-pelvic late hypothesis proposed from the summed synapomorphy approach; however, results suggest limited support for some pectoral branch lengths being significantly longer only early at/after the origin of flight.}, number={2}, journal={SYSTEMATIC BIOLOGY}, author={Clarke, Julia A. and Middleton, Kevin M.}, year={2008}, pages={185–201} }
 @article{ksepka_clarke_devries_urbina_2008, title={Osteology of Icadyptes salasi, a giant penguin from the Eocene of Peru}, volume={213}, ISSN={["1469-7580"]}, DOI={10.1111/j.1469-7580.2008.00927.x}, abstractNote={Abstract}, number={2}, journal={JOURNAL OF ANATOMY}, author={Ksepka, Daniel T. and Clarke, Julia A. and DeVries, Thomas J. and Urbina, Mario}, year={2008}, month={Aug}, pages={131–147} }
 @article{dayrat_cantino_clarke_de queiroz_2008, title={Species names in the PhyloCode: The approach adopted by the international society for phylogenetic nomenclature}, volume={57}, ISSN={["1076-836X"]}, DOI={10.1080/10635150802172176}, abstractNote={Edwards, S. V., L. Liu, and D. K. Pearl. 2007. High resolution species trees without concatenation. Proc. Natl. Acad. Sci. USA 104:5936– 5941. Hennig, W. 1950. Grundzuge Einer Theorie der Phylogenetischen Systematik. Deutscher Zentralverlag, Berlin. [Published in English translation in 1966: Phylogenetic systematics, University of Illinois Press, Urbana, Illinois.] Hudson, R. R. 1983. Testing the constant-rate neutral allele model with protein sequence data. Evolution 37:203–217. Liu, L., and D. K. Pearl. 2007. Species trees from gene trees: Reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Syst. Biol. 56:504–514. Maddison, W. P. 1997. Gene trees in species trees. Syst. Biol. 46:523– 536. Maddison, W. P., and L. L. Knowles. 2006. Inferring phylogeny despite incomplete lineage sorting. Syst. Biol. 55:21–30. Nei, M. 1987. Molecular evolutionary genetics. Columbia University Press, New York. Neigel, J. E. and J. C. Avise. 1986. Phylogenetic relationships of mitochondrial DNA under various demographic models of speciation. Pages 515–534 in Evolutionary processes and theory (S. Karlin and E. Nevo, eds.). Academic Press, Orlando, Florida. Nichols, R. 2001. Gene trees and species trees are not the same. Trends Ecol. Evol. 16:358–364.}, number={3}, journal={SYSTEMATIC BIOLOGY}, author={Dayrat, Benoit and Cantino, Philip D. and Clarke, Julia A. and De Queiroz, Kevin}, year={2008}, pages={507–514} }
 @article{turner_pol_clarke_erickson_norell_2007, title={A basal Dromaeosaurid and size evolution preceding avian flight}, volume={317}, ISSN={["1095-9203"]}, DOI={10.1126/science.1144066}, abstractNote={Fossil evidence for changes in dinosaurs near the lineage leading to birds and the origin of flight has been sparse. A dinosaur from Mongolia represents the basal divergence within Dromaeosauridae. The taxon's small body size and phylogenetic position imply that extreme miniaturization was ancestral for Paraves (the clade including Avialae, Troodontidae, and Dromaeosauridae), phylogenetically earlier than where flight evolution is strongly inferred. In contrast to the sustained small body sizes among avialans throughout the Cretaceous Period, the two dinosaurian lineages most closely related to birds, dromaeosaurids and troodontids, underwent four independent events of gigantism, and in some lineages size increased by nearly three orders of magnitude. Thus, change in theropod body size leading to flight's origin was not unidirectional.}, number={5843}, journal={SCIENCE}, author={Turner, Alan H. and Pol, Diego and Clarke, Julia A. and Erickson, Gregory M. and Norell, Mark A.}, year={2007}, month={Sep}, pages={1378–1381} }
 @article{smith_olson_clarke_2007, title={First Atlantic record of the puffin Cerorhinca (Aves, Alcidae) from the Pliocene of North Carolina}, volume={27}, ISSN={["0272-4634"]}, DOI={10.1671/0272-4634(2007)27[1039:FAROTP]2.0.CO;2}, abstractNote={N. ADAM SMITH, STORRS L. OLSON, and JULIA A. CLARKE; North Carolina State University, Department of Marine, Earth and Atmospheric Sciences, Campus Box 8208, Raleigh, North Carolina 27695–8208 U.S.A., adam_smith@ncsu.edu; National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia 20560–0131 U.S.A., olson@si.edu; North Carolina Museum of Natural Sciences, 11 West Jones St., Raleigh, North Carolina 27601–1029 U.S.A., julia_clarke@ncsu.edu.}, number={4}, journal={JOURNAL OF VERTEBRATE PALEONTOLOGY}, author={Smith, N. Adam and Olson, Storrs L. and Clarke, Julia A.}, year={2007}, month={Dec}, pages={1039–1042} }
 @article{clarke_ksepka_stucchie_urbina_giannini_bertelli_narvez_boyd_2007, title={Paleogene equatorial penguins challenge the proposed relationship between biogeography, diversity, and Cenozoic climate change}, volume={104}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.0611099104}, abstractNote={
            New penguin fossils from the Eocene of Peru force a reevaluation of previous hypotheses regarding the causal role of climate change in penguin evolution. Repeatedly it has been proposed that penguins originated in high southern latitudes and arrived at equatorial regions relatively recently (e.g., 4–8 million years ago), well after the onset of latest Eocene/Oligocene global cooling and increases in polar ice volume. By contrast, new discoveries from the middle and late Eocene of Peru reveal that penguins invaded low latitudes >30 million years earlier than prior data suggested, during one of the warmest intervals of the Cenozoic. A diverse fauna includes two new species, here reported from two of the best exemplars of Paleogene penguins yet recovered. The most comprehensive phylogenetic analysis of Sphenisciformes to date, combining morphological and molecular data, places the new species outside the extant penguin radiation (crown clade: Spheniscidae) and supports two separate dispersals to equatorial (paleolatitude ≈14°S) regions during greenhouse earth conditions. One new species,
            Perudyptes devriesi
            , is among the deepest divergences within Sphenisciformes. The second,
            Icadyptes salasi
            , is the most complete giant (>1.5 m standing height) penguin yet described. Both species provide critical information on early penguin cranial osteology, trends in penguin body size, and the evolution of the penguin flipper.
          }, number={28}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Clarke, Julia A. and Ksepka, Daniel T. and Stucchie, Marcelo and Urbina, Mario and Giannini, Norberto and Bertelli, Sara and Narvez, Yanina and Boyd, Clint A.}, year={2007}, month={Jul}, pages={11545–11550} }
 @article{clarke_middleton_2006, title={Bird evolution}, volume={16}, number={10}, journal={Current Biology}, author={Clarke, J. and Middleton, K.}, year={2006}, pages={R350–354} }
 @article{clarke_zhou_zhang_2006, title={Insight into the evolution of avian flight from a new clade of Early Cretaceous ornithurines from China and the morphology of Yixianornis grabaui}, volume={208}, ISSN={["1469-7580"]}, DOI={10.1111/j.1469-7580.2006.00534.x}, abstractNote={Abstract}, number={3}, journal={JOURNAL OF ANATOMY}, author={Clarke, JA and Zhou, ZH and Zhang, FC}, year={2006}, month={Mar}, pages={287–308} }
 @article{clarke_tambussi_noriega_erickson_ketcham_2005, title={Definitive fossil evidence for the extant avian radiation in the Cretaceous}, volume={433}, number={7023}, journal={Nature}, author={Clarke, J. A. and Tambussi, C. P. and Noriega, J. I. and Erickson, G. M. and Ketcham, R. A.}, year={2005}, pages={305–308} }
 @article{clarke_norell_dashzeveg_2005, title={New avian remains from the Eocene of Momgolia and the phylogenetic position of the Eogfruidaelia (Aves, Gruoidea)}, number={3494}, journal={American Museum Novitates}, author={Clarke, J. A. and Norell, M. A. and Dashzeveg, D.}, year={2005}, pages={17-} }
 @article{clarke_2004, title={Morphology, phylogenetic taxonomy, and systematics of Ichthyornis and Apatornis (Avialae: Ornithurae).}, volume={286}, number={2004}, journal={Bulletin of the American Museum of Natural History}, author={Clarke, J. A.}, year={2004}, pages={1–179} }
 @article{clarke_norell_2004, title={New avialan remains and a review of the known avifauna from the Late Cretaceous Nemegt Formation of Mongolia}, number={3447}, journal={American Museum Novitates}, author={Clarke, J. A. and Norell, M. A.}, year={2004}, pages={12-} }