Exactly what I was thinking...
_____________________________
Steven Creber
Ph: 03 9474 9243
Fx: 03 9499 8283
-----Original Message-----
From:
On Behalf Of Frank Rheindt
Sent: Thursday, 16 November 2006 11:49 AM
To:
Subject: DNA and splitting
Dear all,
it's great to see this sudden surge of interest in taxonomy, DNA and
phylogenetics on the list. Even though considered dry and uninteresting
by
many, I think it is a topic that birders should familiarize themselves
with
as closely as possible.
I found Tim Murphy's and Andy Adcock's contributions to this discussion
especially helpful and interesting. However, some of the things they
stated
in the current discussion require correction. I am trying to keep these
comments as intelligible as possible, but those who are not fussed about
the
general topic might want to stop reading and press the delete button
now. At
the end of the message, I will also try to point out what this whole
discussion may mean in the context of the potential new fig-parrot
discovery. I am not providing references for these comments, but those
who
are interested in further reading are welcome to ask me for references
off-list.
More than 99% of an organism's DNA is in the nucleus of its cells
(=nuclear
DNA), the rest sits in its mitochondria (little cell organelles
responsible
for the cell's respiration). A large proportion of nuclear DNA
constitutes
so-called "junk DNA", i.e. it is non-functional, it doesn't code for any
proteins. However, contrary to what Tim Murphy stated, mitochondrial DNA
is
generally functional. Indeed, the genes that have been most widely used
in
phylogenetic studies (e.g. cytochrome b) actually bear the names of the
proteins for which they code. As I shall point out below, mitochondrial
DNA
indeed evolves faster than the vast majority of nuclear functional DNA;
however, there are huge stretches of nuclear junk DNA that evolve
hyper-fast, so fast indeed that they may differ between father and son.
These fast-evolving bits include stretches that geneticists call
"microsatellites" and that we use in paternity tests, forensics etc.
As Tim Murphy pointed out correctly, most phylogenetic studies of birds
and
other organisms use mitochondrial DNA (not nuclear DNA), because its has
several properties that make it more suitable. One of these properties
is
"maternal inheritance", i.e. mitochondrial DNA (=mtDNA) is only passed
on
from mother to offspring, never from the father.
This maternal inheritance of mtDNA brings along advantages, e.g. it
takes a
lot less time for mitochondrial DNA to converge onto a common sequence
in
isolated bird lineages. This is what phylogeneticists term "reciprocal
monophyly". As an example, mtDNA is more likely to show you three
different
and distinct lineages of Shrike-Tit in Australia, whereas nuclear genes
might throw all three of them into one basket, because nuclear genes
require
many more millions of years to attain "reciprocal monophyly". (Note that
I
am just guessing here, because I don't recall that anyone has published
any
DNA study on Shrike-tits so far).
As an aside, maternal inheritance in mitochondrial DNA also conveys
disadvantages, e.g. it is prone to show you the wrong species pedigree
(=species tree) if there have been ancient hybridization events during
which
the mtDNA of one species might have swept out the entire mtDNA of the
other.
Even though both species may have ceased to hybridize a long time ago
and
continued on as different species, they may still show the same mtDNA.
This
is what has probably happened in Pomarine and Great Skua (which have
equal
mtDNA, even though nuclear DNA is very divergent and shows the Pomarine
Skua
to be closely related to the jaegers) and in
White-crowned/Golden-crowned
Sparrows in North America. Indeed, as Leo Joseph and colleagues showed
in
their latest 2006 publication on White-browed and Masked Woodswallow (in
the
Journal of Avian Biology), these two species have identical mtDNA, and
even
though he points out other potential reasons for this, I think that
ancient
hybridization is possibly the best explanation for this pattern.
In response to Andy Adcock's remarks about cut-off boundaries of mtDNA
divergences for species level boundaries, I think it is very misleading
to
give a percent boundary that is supposed to hold across all birds, and
even
more misleading to call it some decimal number such as 2.4 which conveys
a
level of accuracy that we are impossible to come up with. My apologies
to
Andy for the harsh wording, and I hope he won't take it personally, but
I
just think these wide-range cut-off rates are a very dangerous thing in
taxonomy. Why? Read below.
The last ten years have seen quite a few studies demonstrating 2% mtDNA
difference between birds that have been separated for 1 million years.
The
first who came up with this 2% rate were Fleischer and co-workers, who
dated
the splits between Hawaiian honeycreepers according to the age of the
different islands that is known from geological datings. This
"traditional
2% rule" has also been considered a convenient cut-off date for
species-level, as it has been shown to coincide with species boundaries,
first among North American songbirds, and later in many other bird
lineages
all over the world.
However, new studies have taught us better than that, and we now know
that
the rate of mtDNA evolution varies widely among different bird lineages.
A
study of sunbirds from Africa showed that their mtDNA differs at 5.4%
per
million years, and another study on seabirds has come up with three
widely
different rates for albatrosses, shearwaters and storm-petrels, with a
clear
trend towards slower mtDNA evolution at larger body size. Indeed, a
recent
influential study published in a high-caliber journal argues that the
rate
of mtDNA evolution is directly proportional to metabolism and body mass.
What does this mean for ornithology? It means that 0.1% divergence
between
two swallows may be meaningless, whereas it could mean million(s) of
years
of separation for two albatross taxa. Indeed, if you apply the 2% rule
on
ducks of the genus Anas, you would have to lump Pintail, Mallard,
Garganey
and Black Duck all into one species. Clearly there is no universal 2%
rule,
and the adequate rate for species-level boundaries has to be determined
for
each family, maybe even each genus separately.
What does this mean for the potential new fig-parrot? If and once DNA
material is obtained, one can certainly look at the differences in DNA
divergence between it and all the other Australian and New Guinean taxa.
Parrots are known for their long generation times, which suggests a slow
rate of DNA evolution, however, fig-parrots are clearly towards the
lower
end of parrot body size, which may mean higher rates of DNA evolution
from
other parrots (see above). Therefore, any DNA divergence number may be
meaningless for species designation of this potentially new parrot
unless
the authors have sampled mtDNA from other fig-parrots that are known to
be
good (albeit closely related) species in order to compare rates.
Anything
else may just amount to cutting a paper into 5cm strips without a ruler.
Sorry for this overly long message, and good birding to everyone.
Cheers
Frank
---------------------------------------------
============Frank E. RHEINDT================
DEPARTMENT OF GENETICS
University of Melbourne
POSTAL ADDRESS:
Museum Victoria - Sciences Department
GPO Box 666
Melbourne 3001
Victoria
Australia
=============================================
>From: "Tim Murphy" <>
>CC: <>
>Subject: RE: [Birding-Aus] Fig Parrot species
>Date: Wed, 15 Nov 2006 18:20:32 +1000
>
>The DNA analysys for sibling species is best done with mitocondrial DNA
as
>it changes faster..
>
>AS you will know, most DNA is silent (has no know biological function)
and
>so you can compare mtDNA in the same silent gap for many related
species.
>It
>is an oversimplification to say that <x% difference - same species, >x%
>different species, but that is the rough idea.
>
>Googel will
>
>-----Original Message-----
>From:
> Behalf Of Evan Beaver
>Sent: Wednesday, 15 November 2006 5:58 PM
>Cc:
>Subject: Re: [Birding-Aus] Fig Parrot species
>
>
>At the risk of getting too technical, how does DNA evidence
prove/disprove
>whether or not they are the same species? Given that DNA is just a
sequence
>of genes do they just draw a line 40 genes along the sequence and
declare
>"if it's the same to here they are the same species". DNA or otherwise,
>isn't species level classification a biological construct based on
grouping
>similarities?
>
>Evan
>
>On 11/14/06, Michael Todd <> wrote:
> >
> > Hello all,
> >
> > Yep, the DNA results will be very interesting. I think everybody
needs
> > to calm down about the fig parrot debate. We should all just wait
and
> > see what comes out.
> >
> > Incidentally, I was talking to Glenn Holmes this evening . He
reported
> > 10 Swinhoe's Snipe, 1 Wood Sandpiper and 3 Marsh Sandpiper from
Hasties
> > Swamp on the Atherton Tableland today.
> >
> > Cheers
> >
> > Mick
> >
> > Michael Todd
> > Wildlifing Images & Sounds of Nature
> > Latest Additions: Barking Owl, Splendid Fairy-wren, Mulga Parrot
> > www.wildlifing.com
> > Toronto, NSW, Australia O41O 123715
> >
> >
> > Carl Clifford wrote:
> > > Well, this seems to be the logical way to determine the
authenticity
> > > of the proposed species/sub-species. I will wait for such evidence
> > > before making my mind up.
> > > Carl Clifford
> > >
> > > On 14/11/2006, at 12:11 PM, Tim Murphy wrote:
> > >
> > > Yes.
> > >
> > > Tim Murphy
> > >
> > > -----Original Message-----
> > > From:
> > > Behalf Of michael
hunter
> > > Sent: Tuesday, 14 November 2006 11:00 AM
> > > To: Syd Curtis;
> > > Subject: Re: [Birding-Aus] Fig Parrot species
> > >
> > >
> > > Hi All,
> > > Can DNA analysis can be performed on feathers or faeces?
> > > If so, and if John found a nesting-hole as reported,
and
> > > someone
> > > to climb up into the clouds, the species dilemma could quickly be
> > > resolved.
> > > Cheers
> > > Michael
> > >
> > > ===============================
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> > > birding-aus.blogspot.com
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>
>--
>Evan Beaver
>Lapstone, Blue Mountains, NSW
>lat=-33.77, lon=150.64
>===============================
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