The way population is estimated is essentially just comparing how much
genetic diversity there is between species. Low genetic diversity implies
a small population, while high genetic diversity implies a bigger
population. There are a number of biological assumptions required for this
to work though. In particular it assumes that that population trends have
been consistent in recent years, and that the species is a "K" species (has
few offspring and relatively stable populations, rather than many offspring
and a boom and bust cycle).
If you can get a good estimate of the rate of genetic change over time (and
we do have that), and you have a good estimate of the amount of genetic
diversity between some individuals, you can use statistical methods to
create a predictive model of the size the population (which will take into
account the possibility of by chance only taking samples from closely
related birds within a much larger population). There's certainly
uncertainty, but unless Night Parrots have a significantly different mating
behaviour to their nearest relatives, or the population has changed very
significantly very recently, an estimate should within an order of
magnitude.
You don't need to individually map the entire genome to determine genetic
diversity. The easiest technique is to extract DNA and replicate it, and
then cut it up into smaller bits and check the differences in the ratios of
the weights of each small sections of DNA. This is what the "lines" you
see on DNA test on TV are - just cut up segments of DNA that have been
placed on an electrolysed agar sheet and have along the sheet at different
speeds depending on their weight. Of course there are much more
sophisticated techniques which give you a better picture too. I'd have to
go back to the text books to remember which would be best here :P
Jeremy
On 12 August 2013 11:57, colin trainor <> wrote:
> Hi Peter,
>
> I don't understand either, but it is not a simple analysis like
> determining sex, or whether one species is different to another. The key
> element is good quality tissue to begin with. I think that means that
> contemporary samples are needed, and that would also include the molecular
> "footprint" of the species undoubted decline [if there is one showing in
> the molecules, we can assume that this is likely] since roughly 1890
> (perhaps before).
>
> I'm familiar with one molecular study that compared Australian Zebra
> Finch [Genome known!], with Lesser Sundas Zebra Finch (usually still
> considered one species, which is fair). They compared about 30 Aust birds
> (sample specimens) from several sites, with 12 birds from Lombok and Timor
> - Indonesia [tissue specimens well preserved]. The study estimated that 9
> individual Zebra finches colonised the Lesser Sundas from Australia, that
> that occurred at an estimated 1.9 million yrs before present (95% interval:
> 1.2-2.8 million years); and that the current Lesser Sunda population is
> around 18000-26000 birds; and the Australian population at 1.3 million and
> 7 million (using different analyses). These are only estimates [not
> necessarily "reality"], based on the analysis with the many assumptions and
> limitations discussed.
>
> I guess it does highlight the difficulties/complexities of such a study,
> even with the best (or second best) known bird species on the planet.
>
> Colin
>
>
>
> > From:
> > To: ; ;
>
> > Date: Mon, 12 Aug 2013 11:39:17 +1000
> > Subject: RE: [Birding-Aus] DNA confirms elusive Night Parrot found
> >
> > Thanks for all that, Colin. I don't understand how DNA analysis gives a
> population estimate. Is it to do with the number of ancestors each bird
> must have had in order to have that amount of variation in its DNA?
> >
> > And if you could get the necessary samples, would you know when that
> population estimate was valid for? I assume the estimate derived from, say,
> 20 samples collected 100 years ago would be no different to 20 collected
> today, yet the population is likely different today to 100 years ago. Even
> 100 years ago there might have been a tiny fraction of the population 200
> years ago.
> >
> > Peter Shute
> >
> > > -----Original Message-----
> > > From:
> > > On Behalf Of
> > > colin trainor
> > > Sent: Monday, 12 August 2013 10:06 AM
> > > To: Ross Macfarlane (TPG);
> > > Subject: [Birding-Aus] DNA confirms elusive Night Parrot found
> >
> > > Determining NParrot populations from bits of existing
> > > specimens would be problematic (recognising their incredible
> > > value and fact you don't want major
> > > damage) ie. availability of tiny bits of dried
> > > [non-preserved, and therefore with DNA increasingly degraded]
> > > flesh from "footpads" or from within a feather - most likely
> > > from specimens
> > > >100 years old.
> > >
> > > Samples size - if you could get some fresh or well preserved
> > > NParrot tissue or blood, you might get an estimate of
> > > population number, but probably with very broad confidence
> > > limits (e.g. with one bird - Result = 10,000 individuals,
> > > made up 95% confidence limits = population is within the
> > > range 100 to 20,000 birds), but with additional samples it
> > > may get closer to reality, and narrower confidence limits.
> > >
> > > You might need say 3-5 samples to get an ?ok result, but need
> > > more to refine it. Sample size would be critical is getting
> > > an estimate close to "reality".
> > >
> > >
> > >
> > >
> > >
> > > > From:
> > > > To: ;
> > > > Subject: Re: [Birding-Aus] DNA confirms elusive Night Parrot found
> > > > Date: Sun, 11 Aug 2013 11:48:08 +1000
> > > >
> > > > Colin, it's actually very feasible, in fact highly
> > > important DNA has
> > > > been extracted from early human fossils that are 100s or
> > > thousands of
> > > > years old, that has been used to build a picture of human
> > > evolution.
> > > > DNA extracted from frozen mammoth carcases in Siberia have
> > > led to some
> > > > researchers to propose reviving mammoth as a species (I truly hope
> > > > this does not happen, but that's not a discussion for
> > > here.) The same
> > > > has been proposed for thylacines using DNA extracted from
> > > preserved joeys in museums.
> > > >
> > > > In other words recovery of DNA from museum specimens is
> > > > well-established science. It doesn't need to be a complete genome,
> > > > just enough long fragments to distinguish night parrot from its
> > > > closest relatives (presumably ground parrot and western ground
> > > > parrot.)
> > > >
> > > > Also distinguishing between human and parrot DNA would be a very
> > > > simple exercise - much more so than for ancient humans as
> > > described above.
> > > > Basically the scientists can look at a series of bands on a
> > > screen and
> > > > see which ones are human and which non-human, almost as
> > > easily as they
> > > > could distinguish a human and a bird footprint.
> > > >
> > > > -----Original Message-----
> > > > From: colin trainor
> > > > Sent: Saturday, August 10, 2013 7:15 PM
> > > > To:
> > > > Subject: [Birding-Aus] DNA confirms elusive Night Parrot found
> > > >
> > > > DNA - Most specimens (?all but 3 perhaps) collected before 1900, so
> > > > not sure how useful it would be.
> > > >
> > > > I'm ignorant of molecular approaches, but this detailed type of
> > > > analysis may not be possible on gnarly old specimens
> > > (?better on blood
> > > > and fresh tissue? - of which there is none)
> > > >
> > > > >>>>>>>>>>>>
> > > >
> > > > To:
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > Subject:
> > > >
> > > > DNA confirms elusive Night Parrot found
> > > >
> > > >
> > > >
> > > >
> > > > From:
> > > >
> > > > Andrew Hobbs <>
> > > >
> > > >
> > > >
> > > >
> > > > Date:
> > > >
> > > > Sat, 10 Aug 2013 14:22:41 +0800
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > There are apparently 22 known specimens in various museums
> > > around the
> > > > world. I would think it quite possible to use DNA analysis
> > > on those
> > > > to make some estimates of population sizes etc. and their
> > > relationship
> > > > to the recent samples. I would be surprised if that is not already
> > > > being done or at least considered.
> > > > Cheers
> > > >
> > > > Andrew
> > > >
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> > >
> > >
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