Re: What goes around comes around

Preston:

> Here's the ref I was thinking of. These guys found over 900 orthologous
> insertions in a 1.5 Mb alignment of human and chimp. So, extrapolating
> we're talking millions, really. The total number in a set of 9 species
> that were fully sequenced in this segment contained over 1000 sites. The
> total is not much higher for the whole group, because the more distant
> species (dog, cat, cow etc) contained only a few sites in this region.
> This is the same data that Frances Collins referred to in his PSCF
> article. If I remember right there were ~50 anomalous insertions in the
> nine species set, but I'm not sure. This is a complicated paper and I
> haven't studied it carefully yet. I'm sure you will find much to object
> to. :)
>
> Genome Res. 2005 Jul;15(7):998-1006.
>
> Orthologous repeats and mammalian phylogenetic inference.
> Bashir A, Ye C, Price AL, Bafna V.
>
> Determining phylogenetic relationships between species is a difficult
> problem, and many phylogenetic relationships remain unresolved, even among
> eutherian mammals. Repetitive elements provide excellent markers for
> phylogenetic analysis, because their mode of evolution is predominantly
> homoplasy-free and unidirectional. Historically, phylogenetic studies
> using repetitive elements have relied on biological methods such as PCR
> analysis, and computational inference is limited to a few isolated
> repeats. Here, we present a novel computational method for inferring
> phylogenetic relationships from partial sequence data using orthologous
> repeats. We apply our method to reconstructing the phylogeny of 28
> mammals, using more than 1000 orthologous repeats obtained from sequence
> data available from the NISC Comparative Sequencing Program. The resulting
> phylogeny has robust bootstrap numbers, and broadly matches results from
> previous studies which were obtained using entirely different data and
> methods. In addition, we shed light on some of the debatable aspects of
> the phylogeny. With rapid expansion of available partial sequence data,
> computational analysis of repetitive elements holds great promise for the
> future of phylogenetic inference.

Preston:

These results are predicated on the assumption that evolution is true. Of
course there is nothing wrong with this (Kuhn calls it "normal science"),
but we need to be careful in using the results outside of normal science;
that is, as evidence for evolution.

In this case, when genomes were first being studied and people started
systematically looking at SINEs, they knew of no insertion site preference
and the SINEs appeared at the same locus in similar species. So, assuming
evolution is true, the obvious interpretation is that these derive from a
common ancestor rather than from independent insertion events in the two
lineages. So you had statements like this being made about 5 years ago:

"There is no compelling empirical or theoretical reason to expect SINEs to
commonly insert at the exact same locus or be transferred or removed from
the genome in any way that is ambiguous by standard methods of experimental
detection." [Shedlock, A.M., Milinkovitch, M.C., Okada, N., "SINE Evolution,
Missing Data, and] the Origin of Whales," Syst. Biol. 49(4):808-817, 2000
(page 810).

This statement has, imbedded in it, the assumption that evolution is true.
Lift that assumption, and things become less obvious. In fact, since then,
SINEs have been found at the same insertion site in distant species, such
that common descent cannot be the cause. In these cases, even those who
presuppose evolution is true must agree that there is something going on,
such as an insertion site preference.

But because of the history of thought here in the past decade or so, the
assumption remains that SINEs (generally) do not have insertion site
preferences. The cases where insertion site preference is unavoidable, even
under evolution, are viewed as the exceptions, not the rule. So here is the
opening statement of the paper you referenced:

"Repetitive elements, particularly SINEs (short interspersed elements) and
LINEs (long interspersed elements), provide excellent markers for
phylogenetic analysis: their mode of evolution is predominantly
homoplasy-free, since they do not typically insert in the same locus of two
unrelated lineages, and unidirectional, since they are not precisely excised
from a locus with the flanking sequences preserved (Shedlock and Okada
2000)."

Fine, but we must not lose track of the history. This is work that in normal
science, where evolution is presumed to be true. If we lifted that
assumption, then here is what I think the theory-neutral interpretation
would be.

The finding of SINEs at homologous insertion sites is evidence either for
common descent or for insertion site preference (simply put: same ancestor
or same process). However, even under the common descent hypothesis, we must
admit that striking common process occurs at least sometimes. So we have no
obvious theoretical reason to rule out common process as the explanation
more generally.

Common process seems to be the more parsimonious explanation. In any case,
this evidence needs to be thrown in with all the other evidence, where we
find significant problems for common descent.

--Cornelius

>
>
> But wait! There's more!
> Here's a bonus. This is new. I haven't read it yet.
>
> Genome Res. 2005 Sep;15(9):1243-9.
>
> Genomic deletions and precise removal of transposable elements mediated by
> short identical DNA segments in primates.
>
> van de Lagemaat LN, Gagnier L, Medstrand P, Mager DL.
>
>
> Insertion of transposable elements is a major cause of genomic expansion
> in eukaryotes. Less is understood, however, about mechanisms underlying
> contraction of genomes. In this study, we show that retroelements can, in
> rare cases, be precisely deleted from primate genomes, most likely via
> recombination between 10- to 20-bp target site duplications (TSDs)
> flanking the retroelement. The deleted loci are indistinguishable from
> pre-integration sites, effectively reversing the insertion. Through
> human-chimpanzee-Rhesus monkey genomic comparisons, we estimate that
> 0.5%-1% of apparent retroelement "insertions" distinguishing humans and
> chimpanzees actually represent deletions. Furthermore, we demonstrate that
> 19% of genomic deletions of 200-500 bp that have occurred since the
> human-chimpanzee divergence are associated with flanking identical repeats
> of at least 10 bp. A large number of deletions internal to Alu elements
> were also found flanked by homologies. These results suggest that
> illegitimate recombination between short direct repeats has played a
> significant role in human genome evolution. Moreover, this study lends
> perspective to the view that insertions of retroelements represent
> unidirectional genetic events.
Received on Sat Oct 8 12:36:29 2005