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Transposons papers

Some avian data. Haven't looked it through, but the
abstracts seem relevant.

Insertion Events of CR1 Retrotransposable Elements
Elucidate the Phylogenetic Branching Order in
Galliform Birds
Kaiser, Vera B.; van Tuinen, Marcel; Ellegren, Hans
Molecular Biology and Evolution, Volume 24, Number 1,
January 2007 , pp. 338-347(10)

Using standard phylogenetic methods, it can be hard to
resolve the order in which speciation events took
place when new lineages evolved in the distant past
and within a short time frame. As an example,
phylogenies of galliform birds (including well-known
species such as chicken, turkey, and quail) usually
show low bootstrap support values at short internal
branches, reflecting the rapid diversification of
these birds in the Eocene. However, given the key role
of chicken and related poultry species in
agricultural, evolutionary, general biological and
disease studies, it is important to know their
internal relationships. Recently, insertion patterns
of transposable elements such as long and short
interspersed nuclear element markers have proved
powerful in revealing branching orders of difficult

Here we decipher the order of speciation events in a
group of 27 galliform species based on insertion
events of chicken repeat 1 (CR1) transposable
elements. Forty-four CR1 marker loci were identified
from the draft sequence of the chicken genome, and
from turkey BAC clone sequence, and the presence or
absence of markers across species was investigated via
electrophoretic size separation of amplification
products and subsequent confirmation by DNA
sequencing. Thirty markers proved possible to type
with electrophoresis of which 20 were phylogenetically
informative. The distribution of these repeat elements
supported a single homoplasy-free cladogram, which
confirmed that megapodes, cracids, New World quail,
and guinea fowl form outgroups to Phasianidae and that
quails, pheasants, and partridges are each
polyphyletic groups. Importantly, we show that chicken
is an outgroup to turkey and quail, an observation
which does not have significant support from previous
DNA sequence- and DNA-DNA hybridization-based trees
and has important implications for evolutionary
studies based on sequence or karyotype data from
galliforms. We discuss the potential and limitations
of using a genome-based retrotransposon approach in
resolving problematic phylogenies among birds. 

DOI: 10.1093/molbev/msl164

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.

We improve the taxon sampling for avian phylogeny by
analyzing 7 new mitochondrial genomes (a toucan,
woodpecker, osprey, forest falcon, American kestrel,
heron, and a pelican). This improves inference of the
avian tree, and it supports 3 major conclusions. The
first is that some birds (including a parrot, a
toucan, and an osprey) exhibit a complete duplication
of the control region (CR) meaning that there are at
least 4 distinct gene orders within birds. However, it
appears that there are regions of continued gene
conversion between the duplicate CRs, resulting in
duplications that can be stable for long evolutionary
periods. Because of this stable duplicated state, gene
order can eventually either revert to the original
order or change to the new gene order. The existence
of this stable duplicate state explains how an
apparently unlikely event (finding the same novel gene
order) can arise multiple times. Although rare genomic
changes have theoretical advantages for tree
reconstruction, they can be compromised if these
apparently rare events have a stable intermediate
state. Secondly, the toucan and woodpecker improve the
resolution of the 6-way split within Neoaves that has
been called an ‘‘explosive
radiation.’’ An explosive radiation
implies that normal microevolutionary events are
insufficient to explain the observed macroevolution.
By showing the avian tree is, in principle,
resolvable, we demonstrate that the radiation of birds
is amenable to standard evolutionary analysis.
Thirdly, and as expected from theory, additional taxa
breaking up long branches stabilize the position of
some problematic taxa (like the falcon). In addition,
we report that within the birds of prey and allies, we
did not find evidence pairing New World vultures with
storks or accipitrids (hawks, eagles, and osprey) with


I think I have the PDFs.


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