Introns outperform exons in analyses of basal avian phylogeny using clathrin heavy chain genes

Chojnowski, Jena L.; Kimball, Rebecca T.; Braun, Edward L.

doi:10.1016/j.gene.2007.11.016

Cited by 80 publications

(93 citation statements)

References 34 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The primers presented here expand those published previously (Harshman et al, 2003;Barker, 2004;Driskell and Christidis, 2004;Zink et al, 2006;Cox et al, 2007;Barker et al, 2008;Chojnowski et al, 2008;Yuri et al, 2008;Hackett et al, 2008) in several major ways. First, we provide additional primers to expand the utility of published loci, including alternative primers and internal primers that are anchored in highly conserved regions and can also be used both for nested PCR and to obtain shorter segments.…”

Section: Loci and Primerssupporting

confidence: 74%

See 1 more Smart Citation

A well-tested set of primers to amplify regions spread across the avian genome

Kimball

Braun

Barker

et al. 2009

Molecular Phylogenetics and Evolution

Self Cite

165

100

View full text Add to dashboard Cite

Section: Loci and Primerssupporting

confidence: 74%

“…1). We have already collected a substantial dataset from these regions (e.g., Chojnowski et al, 2008;Yuri et al, 2008;Hackett et al, 2008), providing outgroups and a backbone for future studies that utilize the same regions.…”

Section: --mentioning

confidence: 99%

A well-tested set of primers to amplify regions spread across the avian genome

Kimball

Braun

Barker

et al. 2009

Molecular Phylogenetics and Evolution

Self Cite

165

100

View full text Add to dashboard Cite

“…Furthermore, our conclusions do not reflect the specific set of outgroups used; analyses including crocodilians ( Fig. 2) and/or up to 150 additional neognaths, representing all major living avian lineages, also support ratite polyphyly (25,26,30). Separate analyses of individual loci show that 19 of 20 support paleognath monophyly in all analytical approaches (data not shown).…”

Section: Resultsmentioning

confidence: 69%

“…S5) is found in ratites (including ostrich) but not tinamous, thus conflicting with the other indels and analyses of nucleotide substitutions. Vertebrate indels consistently exhibit less homoplasy than nucleotide substitutions (26,34), and an examio A group is polyphyletic if its defining characters are convergent (29). Ratites have long been defined by the absence of a keel on their sternum (e.g., ref.…”

Section: Resultsmentioning

confidence: 99%

“…We assembled a dataset of 20 nuclear loci widely dispersed in the avian genome [supporting information (SI) Table S1] to examine ratite monophyly. It contains Ϸ30% protein-coding and 70% noncoding sequence (Table S1), taking advantage of the phylogenetic signal in archosaur noncoding sequences (26)(27)(28). The dataset comprises 18 taxa, including all extant ratite genera, four tinamou genera, and eight outgroup taxa (Table S2).…”

mentioning

confidence: 99%

See 1 more Smart Citation

Phylogenomic evidence for multiple losses of flight in ratite birds

Harshman

Braun

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

195

227

View full text Add to dashboard Cite

Ratites (ostriches, emus, rheas, cassowaries, and kiwis) are large, flightless birds that have long fascinated biologists. Their current distribution on isolated southern land masses is believed to reflect the breakup of the paleocontinent of Gondwana. The prevailing view is that ratites are monophyletic, with the flighted tinamous as their sister group, suggesting a single loss of flight in the common ancestry of ratites. However, phylogenetic analyses of 20 unlinked nuclear genes reveal a genome-wide signal that unequivocally places tinamous within ratites, making ratites polyphyletic and suggesting multiple losses of flight. Phenomena that can mislead phylogenetic analyses, including long branch attraction, base compositional bias, discordance between gene trees and species trees, and sequence alignment errors, have been eliminated as explanations for this result. The most plausible hypothesis requires at least three losses of flight and explains the many morphological and behavioral similarities among ratites by parallel or convergent evolution. Finally, this phylogeny demands fundamental reconsideration of proposals that relate ratite evolution to continental drift.convergence ͉ flightlessness ͉ Paleognath ͉ homoplasy ͉ vicariance biogeography

show abstract

Linking the molecular evolution of avian beta (β) keratins to the evolution of feathers

Greenwold

Sawyer

2011

J Exp Zool Pt B

View full text Add to dashboard Cite

Feathers of today's birds are constructed of beta (β)-keratins, structural proteins of the epidermis that are found solely in reptiles and birds. Discoveries of "feathered dinosaurs" continue to stimulate interest in the evolutionary origin of feathers, but few studies have attempted to link the molecular evolution of their major structural proteins (β-keratins) to the appearance of feathers in the fossil record. Using molecular dating methods, we show that before the appearance of Anchiornis (∼155 Million years ago (Ma)) the basal β-keratins of birds began diverging from their archosaurian ancestor ∼216 Ma. However, the subfamily of feather β-keratins, as found in living birds, did not begin diverging until ∼143 Ma. Thus, the pennaceous feathers on Anchiornis, while being constructed of avian β-keratins, most likely did not contain the feather β-keratins found in the feathers of modern birds. Our results demonstrate that the evolutionary origin of feathers does not coincide with the molecular evolution of the feather β-keratins found in modern birds. More likely, during the Late Jurassic, the epidermal structures that appeared on organisms in the lineage leading to birds, including early forms of feathers, were constructed of avian β-keratins other than those found in the feathers of modern birds. Recent biophysical studies of the β-keratins in feathers support the view that the appearance of the subfamily of feather β-keratins altered the biophysical nature of the feather establishing its role in powered flight.

show abstract

Introns outperform exons in analyses of basal avian phylogeny using clathrin heavy chain genes

Cited by 80 publications

References 34 publications

A well-tested set of primers to amplify regions spread across the avian genome

A well-tested set of primers to amplify regions spread across the avian genome

Phylogenomic evidence for multiple losses of flight in ratite birds

Linking the molecular evolution of avian beta (β) keratins to the evolution of feathers

Contact Info

Product

Resources

About