[Taxacom] molecular phylogeny

John Grehan jgrehan at sciencebuff.org
Thu Mar 31 11:14:54 CDT 2011

Some may find the article excerpted below of interest. Given the way the
orangutan theory is trashed because it is not sequence evidence its
always interesting to me to see molecular theorists admit the problems.
Of course this paper is along the lines of "the method does not work,
but only if one has faith in the future that will somehow figure out how
to make it work, then it will.


John Grehan



Resolving Difficult Phylogenetic Questions: Why More

Sequences Are Not Enough


PLoS Biology March 2011 | Volume 9 | Issue 3 | e1000602




In the quest to reconstruct the Tree of Life, researchers have
increasingly turned to phylogenomics, the inference of phylogenetic
relationships using genome-scale data (Box 1). Mesmerized by the
sustained increase in sequencing throughput, many phylogeneticists
entertained the hope that the incongruence frequently observed in

studies using single or a few genes [1] would come to an end with the

of large multigene datasets. Yet, as so often happens, reality has
turned out to be far

more complex, as three recent large-scale analyses, one published in
PLoS Biology

[2-4], make clear. The studies, which deal with the early
diversification of animals, produced highly incongruent (Box 2) findings
despite the use of considerable

sequence data (see Figure 1). Clearly, merely adding more sequences is

enough to resolve the inconsistencies. Here, taking these three studies
as a case

in point, we discuss pitfalls that the simple addition of sequences
cannot avoid, and

show how the observed incongruence can be largely overcome and how

bioinformatics methods can help reveal the full potential of




Contrary to common belief, some degree of conflict has to be expected
when applying phylogenomics to difficult phylogenetic questions, because
of the preva-lence of non-phylogenetic signal. Consequently, we stress
the necessity of reducing

its impact. Since taxon and gene sampling is being rapidly improved by
the relentless

progress in sequencing technology (even if obtaining well preserved and

identified specimens remains the limiting factor for several key taxa),
full achievement

of the ultimate goal of phylogenomics- i.e., accurate resolution of the
Tree of Life-will primarily hinge on better procedures for the selection
of orthologous and least saturated genes as well as on improved models
of sequence evolution. In summary, while we certainly encourage the
inclusion of neglected groups of organisms in large-scale sequencing
studies (e.g., [2,3,46,48]), we consider at least as important that
phylogeneticists engage in theoretical and bioinformatics developments
that keep

pace with sequencing technology to overcome these serious bottlenecks.
This is essential to ensure that lessons learned from classical and
molecular systematics are not forgotten in the phylogenomic era.



Dr. John R. Grehan
Director of Science and Research
Buffalo Museum of Science
1020 Humboldt Parkway
Buffalo, NY 14211-1193

email: jgrehan at sciencebuff.org
Phone: (716) 896-5200 ext 372
Fax: (716) 897-6723


Ghost moth research

Human evolution and the great apes


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