2013:
Smith, J.V., E.L. Braun, R.T. Kimball. 2013. Ratite
nonmonophyly: independent evidence from 40 novel loci. Systematic Biology, 62: 35-49. [full
text]
Yuri, T., R.T. Kimball, J. Harshman,
R.C.K.
Bowie, M.J. Braun, J.L.
Chojnowski,
K.-L.
Han, S.J. Hackett, C.J.
Huddleston, W.S. Moore, S. Reddy, F.H. Sheldon, C.C. Witt, and E.L.
Braun.
2013. Parsimony and model-based analyses of indels in avian nuclear
genes reveal congruent and incongruent phylogenetic signals. Biology, in
press.
2012:
Wang, N., E.L.
Braun, R.T. Kimball. 2012. Testing hypotheses about the sister group of
the passeriformes using an independent 30-locus data set. Molecular Biology and Evolution,
29: 737-750. [full
text]
[supplementary
information]
2011:
Braun, E.L., R.T. Kimball,
K.-L.
Han, N.R. Iuhasz-Velez, A.J. Bonilla, J.L. Chojnowski, J.V. Smith,
R.C.K.
Bowie, M.J. Braun, S.J. Hackett, J. Harshman, C.J. Huddleston, B.D.
Marks, K.J.
Miglia, W.S. Moore, S. Reddy, F.H. Sheldon, C.C. Witt, and T. Yuri.
2011.
Homoplastic microinversions and the avian tree of life. BMC Evolutionary Biology, 11:141. [full
text] [additional
files]
Han, K.-L., E.L. Braun, R.T. Kimball, S. Reddy, R.C.K.
Bowie,
M.J. Braun, J.L. Chojnowski, S.J. Hackett, J. Harshman, C.J.
Huddleston, B.D.
Marks, K.J. Miglia, W.S. Moore, F.H. Sheldon, D.W. Steadman, C.C. Witt,
and T.
Yuri. 2011. Are transposable element insertions homoplasy free?: An
examination
using the avian tree of life. Systematic
Biology, 60: 375-386.
Kimball, R.T, C.M. St. Mary,
and
E.L. Braun. 2011. A Macroevolutionary Perspective on Multiple Sexual
Traits in
the Phasianidae (Galliformes). International Journal of
Evolutionary
Biology, Article ID 423938. [full
text with corrigendum]
2010:
Amaral, F.S.R., F.H.
Sheldon, and A.
Wajntal. 2010. Towards an assessment of character
interdependence in avian
RNA phylogenetics: a general secondary structure model for the avian
mitochondrial 16S rRNA. Molecular
Phylogenetics
and
Evolution, 56: 498-506.
Bonilla, A.J., E.L. Braun, and R.T.
Kimball. 2010.
Comparative
molecular
evolution
and
phylogenetic utility of 3'-UTRs and introns
in Galliformes. Molecular
Phylogenetics and
Evolution, 56: 536-542. [full
text]
Han, K.-L., M.B. Robbins,
and M.J.
Braun. 2010. A
multi-gene
estimate of phylogeny in the nightjars and nighthawks
(Caprimulgidae). Molecular Phylogenetics and Evolution,
55:
443-453.
Marks, B. D. 2010. Are
lowland
rainforests really evolutionary museums? Phylogeography of the green
hylia
(Hylia prasina) in the
Afrotropics.
Molecular Phylogenetics and Evolution,
55:
178-184.
2009:
Amaral, F.S.R., F.H.
Sheldon, A.
Gamauf, E. Haring, M.J. Riesing, L.F. Silveira, and A. Wajntal.
2009.
Patterns and processes of diversification in a widespread and
ecologically
diverse avian group, the buteonine hawks (Aves, Accipitridae). Molecular Phylogenetics and Evolution,
53:
703-715.
Katsu Y, E.L. Braun, L.J.
Guillette
Jr., and T. Iguchi. 2009. From reptilian phylogenomics to reptilian
genomes:
analyses of c-Jun and DJ-1 proto-oncogenes.
Cytogenetic and Genome Research, 127:
79-93.
Kimball,
R.T., E.L.
Braun, R.C.K.
Bowie, M.J. Braun, J.L. Chojnowski, S.J. Hackett, K.-L. Han, J.
Harshman, V.
Heimer-Torres, W. Holznagel, C.J. Huddleston, B.D. Marks, K.J. Miglia,
W.S.
Moore, S. Reddy, F.H. Sheldon, J.V. Smith, C.C. Witt, and T. Yuri.
2009. A set
of resources to amplify nuclear regions across the avian genome. Molecular Phylogenetics and Evolution,
50:
654-660. [full text]
Sheldon, F.H., D. J. Lohman,
H.C.
Lim, F. Zou, S.M. Goodman, D.M. Prawiradilaga, K. Winker, T.M. Braile,
and R.G.
Moyle. 2009. Phylogeography of the magpie-robin species complex (Aves:
Turdidae: Copsychus) reveals
a
Philippine species, an interesting isolating barrier, and unusual
dispersal
patterns in the Indian Ocean and Southeast Asia. Journal of Biogeography
36:1070-1083.
2008:
Chojnowski, J.L., R.T. Kimball, and E.L. Braun. 2008.
Introns
outperform exons in analyses of basal avian phylogeny using clathrin
heavy
chain genes. Gene, 410:
89-96. [full
text]
Chojnowski, J.L. and E.L.
Braun.
2008. Turtle isochore structure is intermediate between amphibians and
other
amniotes. Integrative and
Comparative
Biology, 48: 454-462.
Franklin, J. and D.W.
Steadman. 2008
Prehistoric species richness of birds on oceanic islands. Oikos 117: 1885-1891.
Hackett, S.J., R.T. Kimball,
S.
Reddy, R.C.K. Bowie, E.L. Braun, M.J. Braun, J.L. Chojnowski, W.A. Cox,
K.-L.
Han, J. Harshman, C. Huddleston, B.D. Marks, K.J. Miglia, W.S. Moore,
F.H.
Sheldon, D.W. Steadman, C.C. Witt and T. Yuri. 2008. A phylogenomic
study of
birds reveals their evolutionary history. Science, 320: 1763-1768.
[full text]
[supplementary
information]
Science podcast
by R.T. Kimball
Featured as a News Focus [Pennisi
2008
Science, 320:
1716-7]
Harshman, J., E.L. Braun,
M.J.
Braun, C.J. Huddleston, R.C.K. Bowie, J.L. Chojnowski, S.J. Hackett,
K-L. Han,
R.T. Kimball, B.D. Marks, K.J. Miglia, W.S. Moore, S. Reddy, F.H.
Sheldon, S.J.
Steppan, C.C. Witt, and T. Yuri. 2008. Phylogenomic evidence for multiple losses
of
flight in ratite birds. Proceedings
of the
National Academy of Sciences, 105:13462-13467. [full text]
[supplementary
information]
Kimball, R.T. and E.L.
Braun.
2008.A multigene
phylogeny
of Galliformes supports a single origin of erectile ability in
non-feathered
facial traits. Journal of Avian
Biology, 39: 438-445. [full
text]
Steadman, D.W. 2008. Doves
(Columbidae) and cuckoos (Cuclidae) from the early Miocene of Florida. Bulletin of the Florida Museum of Natural
History, 48: 1-16.
Yuri, T., M.J. Braun, R.T. Kimball, and
E.L.
Braun. 2008. Duplication and accelerated evolution of growth hormone
gene in
passerine birds. Molecular Biology
and
Evolution 25: 352-361. [full
text][supplementary
figure
S1] [excel
file for
supplementary data 1] [excel file for
supplementary
data 1]
NOTE: The originally published title
was an
error (the published erratum is included in the pdf available here)
2007:
Cleere, N., A.W. Kratter,
D.W.
Steadman, M.J. Braun, C.J. Huddleston, C.E. Filardi and G. Dutson.
2007. A new
genus of frogmouth (Podargidae) from the Solomon Islands – results from
a
taxonomic review of Podargus
ocellatus
inexpectatus Hartert 1901. Ibis,
149:271-286.
Cox, W.A., R.T. Kimball, and
E.L.
Braun. 2007. Phylogenetic position of the New World quail
(Odontophoridae): Eight
nuclear loci and three mitochondrial regions contradict morphology and
the
Sibley-Ahlquist tapestry. The Auk,
124:
71-84.
[full
text]
Gibb, G.C., O. Kardailsky,
R.T.
Kimball, E.L. Braun, and D. Penny. 2007. Mitochondrial genomes and avian
phylogeny: Complex
characters and resolvability without explosive radiations. Molecular Biology and Evolution,
24:
269-280. [full
text]
Marks, B.D., J.D. Weckstein,
and
R.G. Moyle. 2007. Molecular phylogenetics of the bee-eaters (Aves:
Meropidae)
based on nuclear and mitochondrial DNA sequence data. Molecular Phylogenetics and Evolution,
45:
23-32.
Moyle, R.G., J. Fuchs, E.
Pasquet,
and B.D. Marks. 2007. Feeding behavior, toe count, and the phylogenetic
relationships among alcedinine kingfishers. Journal of Avian Biology, 38:
317-326.
Whiteman, N.K., R.T.
Kimball, and
P.G. Parker. 2007. Co-phylogeography and comparative population
genetics of the
threatened Galápagos hawk and three ectoparasite species: ecology
shapes
population histories within parasite communities. Molecular Ecology, 16:
4759-4773.
Zou, F.S., H.C. Lim, B.
Marks, R.G.
Moyle, and F.H. Sheldon. 2007. Molecular phylogenetic analysis of the
Grey-cheeked Fulvetta (Alcippe
morrisonia) of China and Indochina: A case of remarkable genetic
divergence in a “species." Molecular
Phylogenetics
and
Evolution, 44:
165-174.
2006:
Kirchman, J.J. and D.W.
Steadman.
2006. Rails (Rallidae: Gallirallus) from prehistoric archaeological
sites in
Western Oceania. Zootaxa,
1316:1-31.
Moyle, R.G, J. Cracraft, M. Lakim, J.
Nais, and
F.H. Sheldon. 2006. Reconsideration of the phylogenetic relationships
of the
enigmatic Bornean Bristlehead (Pityriasis
gymnocephala). Molecular Phylogenetics and
Evolution,39:
893-898.
Moyle, R. G. and B. D.
Marks. 2006.
Phylogenetic relationships of the bulbuls (Aves: Pycnonotidae) based on
mitochondrial and nuclear DNA sequence data. Molecular Phylogenetics and Evolution,
40:
687-695.
Steadman, D.W. 2006. A new species of
extinct
tooth-billed pigeon (Didunculus) from the Kingdom of Tonga, and the
concept of
endemism in insular landbirds. Journal
of
Zoology, 268: 233-241.
Steadman, D. W. 2006.
Extinction and
Biogeography of Tropical Pacific Birds. University of Chicago Press,
Chicago,
IL. 577 pp. + index.[see
at
Amazon]
Steadman, D.W. and Ó.
Carranza-Castañeda. 2006. Early Pliocene to early Pleistocene birds
from
central México. Pp. 61-71 in Ó. Carranza-Castañeda & E.H. Lindsay,
eds.
Advances in Late Tertiary Vertebrate Paleontology in México.
Universidad
Nacional Autónoma de México, Instituto de Geología y Centro de
Geociencias,
Publicación Especial No. 4.
2005:
Kirchman, J.J. and D.W.
Steadman.
2005. Rails (Aves: Rallidae: Gallirallus) from prehistoric sites in the
Kingdom
of Tonga, including description of a new species. Proceedings of the Biological Society of
Washington, 118:465-477.
Steadman, D. W. 2005. The
paleoecology and fossil history of migratory landbirds. pp. 5-17 in
R.S.
Greenberg and P.P. Marra, eds. Birds of Two Worlds. Johns Hopkins
University
Press, Baltimore, MD
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