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Re: Molecular taxonomy for dummies?


concerning retroposons, their nature and utility for phylogenetic
reconstructions, the following review paper might be of help (see citation and
abstract below). Maybe the glossary and the figures facilitate the
understanding of what it's all about. :-)

Although the title focuses on SINEs (short interspersed elements, a special
group of retroposons), the methodological issues apply to other retroposons
(LINEs aka long interspersed elements, LTRs aka long terminal repeat elements)
as well (but not DNA transposons!). In mammals, SINEs have been most commonly
used for phylogenetic reconstructions, simply because they are the most
numerous retroposon insertions.

In birds, there are hardly any SINEs, so you have to use either LINEs (such as
CR1 aka chicken repeat 1 elements) or LTRs.

If you have specific questions, please contact me.

Best regards,


Andrew M. Shedlock, Kazuhiko Takahashi, Norihiro Okada (2006): SINEs of
speciation: tracking lineages with retroposons. Trends in Ecology & Evolution.

"The value of short interspersed elements (SINEs) for diagnosing common
ancestry is being expanded to examine the differential sorting of lineages
through the course of speciation events. Because most SINEs are neutral
markers of identical descent, are not precisely excised from the genome and
have a known ancestral condition, they are advantageous for reconciling gene
trees and species trees with minimal phylogenetic error. A population
perspective on SINE evolution combined with coalescence theory provides a
context for investigating the phenomenon of ancestral polymorphism and its
role in producing incongruent SINE insertion patterns among multiple loci.
Studies of human Alu repeats demonstrate the value of young polymorphic SINEs
for assessing human genomic diversity and tracking ancient demographics of
human populations, whereas incongruent insertion patterns revealed by older
fixed SINE loci, such as those in African cichlid fishes, contain information
that might help identify ancient radiations that are otherwise obscured by
accumulated mutations in sequence data. Here, we review the utility of
retroposons for inferring common ancestry, discuss limits to the method, and
clarify confusion by providing examples from the literature that illustrate
how discordant multi-locus insertion patterns of retroelements can indicate
lineage-sorting events that should not be misinterpreted as phylogenetic

Dr Ronald Orenstein schrieb am 2011-09-26:
> In the course of following (at some considerable distance) the
> discussion on Passeriformes, I am increasingly realizing that I need
> a basic, simple guide to the subject of molecular taxonomy. I mean
> something directed at a poor ignorant fellow like myself who hasn't
> the faintest idea what a retroposon is, or who thinks that long
> branch attraction has something to do with romance. Does such a thing
> exist?

> Ronald Orenstein
> 1825 Shady Creek Court
> Mississauga, ON
> Canada L5L 3W2