I am glad Andy Jones has weighed in on this topic; he is incomparably better
qualified than I to comment on the Hackett, et al. article in Science.  I
would just like emphasize one general point from the point of view of (and
for the benefit of) birders, who are generally not closely acquainted with
genetics.  Nor am I for that matter, I just happen to have a talented
step-daughter who is a geneticist and patiently explains things to me from
time to time.
First, many of the birders who have weighed in on this topic tend to confuse
phenotype and genotype.  This is the old "if it walks like a duck and quacks
like a duck, it must be a duck" school of thought that dates back to before
Linnaeus.  Unfortunately, biology is replete with examples of things that
look very similar, but which are genetically quite distinct, and vice versa.


The key objective in taxonomy is to find an objective measure of the
differences between organisms.  In the nineteenth century, it was thought
that morphological measurements, properly arranged, would disclose the
relationships between groups of living entities.  By and large, they pretty
much got it right, but problems remained.

Sibley and Ahlquist's DNA-DNA hybridization studies of the 80's were a big
step forward and led to some deep insights into bird relationships.
 However, the DNAs of two different species can hybridize in a gazillion
ways and each way will have a different dissociation temperature.  The
resulting noise in the measurements limits the resolution of the
distinctions that can be made.

The newer nucleotide sequencing techniques are based on the question "how
many substitutions would I have to make to turn this gene into that one?"
 If many substitutions are necessary, the species must not be closely
related.  As Andy points out, 19 nuclear loci is a huge advance over most
studies.  By contrast, the genetic "bar coding" project that stirred up so
much buzz two years ago used no more than 600 base pairs on one locus of the
mitochondrial DNA.

The Hackett study is an enormous advance in resolution, but it too leaves
some unanswered questions.  Andy mentions the time-honored conundrum  of the
Hoatzin, the bizarre South American bird that clambers around in trees using
the claws on its wings.  The new study also cannot confidently place the
pigeons and doves, a widespread and numerous family known to just about
every human on the planet.

So the search goes on.  With faster sequencers, better statistical
methods, and bigger computers, we may one day be able to answer these
questions.  Then we can move on to defining just what a species is and how
come those ducks and gulls hybridize so easily.

For those of you who can stand a little more depth, I recommend Devorah
Bennu's blog

http://scienceblogs.com/grrlscientist/2008/06/early_birds_shake_up_avian_tre.php

for a nifty synopsis of the Hackett paper, including some nice graphics that
dramatically illustrate the relationships between the clades.

Cheers,

Bob




--
Robert D Powell
Wilmington, OH, USA
[log in to unmask]
http://rdp1710.wordpress.com

Nulla dies sine linea

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