Dynamic evolution of base composition: causes and consequences in avian phylogenomics.
Abstract
Resolving the phylogenetic relationships among birds is a classical problem in systematics,
and this is particularly so when it comes to understanding the relationships among
Neoaves. Previous phylogenetic inference of birds has been limited to mitochondrial
genomes or a few nuclear genes. Here, we apply deep brain transcriptome sequencing
of nine bird species (several passerines, hummingbirds, dove, parrot, and emu), using
next-generation sequencing technology to understand features of transcriptome evolution
in birds and how this affects phylogenetic inference, and combine with data from two
bird species using first generation technology. The phylogenomic data matrix comprises
1,995 genes and a total of 0.77 Mb of exonic sequence. First, we find an unexpected
heterogeneity in the evolution of base composition among avian lineages. There is
a pronounced increase in guanine + cytosine (GC) content in the third codon position
in several independent lineages, with the strongest effect seen in passerines. Second,
we evaluate the effect of GC content variation on phylogenetic reconstruction. We
find important inconsistencies between the topologies obtained with or without taking
GC variation into account, each supporting different conclusions of past studies and
also influencing hypotheses on the evolution of the trait of vocal learning. Third,
we demonstrate a link between GC content evolution and recombination rate and, focusing
on the zebra finch lineage, find that recombination seems to drive GC content. Although
we cannot reveal the causal relationships, this observation is consistent with the
model of GC-biased gene conversion. Finally, we use this unparalleled amount of avian
sequence data to study the rate of molecular evolution, calibrated by fossil evidence
and augmented with data from alligator transcriptome sequencing. There is a 2- to
3-fold variation in substitution rate among lineages with passerines being the most
rapidly evolving and ratites the slowest. This study illustrates the potential of
next-generation sequencing for phylogenomic studies but also the pitfalls when using
genome-wide data with heterogeneous base composition.
Type
Journal articleSubject
AnimalsBase Composition
Birds
Codon
Evolution, Molecular
Genomics
Phylogeny
Proteome
Recombination, Genetic
Transcriptome
Permalink
https://hdl.handle.net/10161/11239Published Version (Please cite this version)
10.1093/molbev/msr047Publication Info
Nabholz, Benoit; Künstner, Axel; Wang, Rui; Jarvis, Erich D; & Ellegren, Hans (2011). Dynamic evolution of base composition: causes and consequences in avian phylogenomics.
Mol Biol Evol, 28(8). pp. 2197-2210. 10.1093/molbev/msr047. Retrieved from https://hdl.handle.net/10161/11239.This is constructed from limited available data and may be imprecise. To cite this
article, please review & use the official citation provided by the journal.
Collections
More Info
Show full item recordScholars@Duke
Erich David Jarvis
Adjunct Professor in the Deptartment of Neurobiology
Dr. Jarvis' laboratory studies the neurobiology of vocal communication. Emphasis is
placed on the molecular pathways involved in the perception and production of learned
vocalizations. They use an integrative approach that combines behavioral, anatomical,
electrophysiological and molecular biological techniques. The main animal model used
is songbirds, one of the few vertebrate groups that evolved the ability to learn vocalizations.
The generality of the discoveries is tested in other vocal lear

Articles written by Duke faculty are made available through the campus open access policy. For more information see: Duke Open Access Policy
Rights for Collection: Scholarly Articles
Works are deposited here by their authors, and represent their research and opinions, not that of Duke University. Some materials and descriptions may include offensive content. More info