
DNA analysis reveals there are four distinct giraffe species, not one - Jerry2
https://www.researchgate.net/blog/post/dna-analysis-reveals-there-are-four-distinct-giraffe-species-not-one-as-previously-thought
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sndean
I'm pretty happy with a (the?) species definition in microbiology:

<97% 16S rRNA gene sequence identity? You're a different species [0].

It's a little more complicated than that, and some important people
(especially in the older generation) don't like it, but it's a good / quick
standard.

[0]
[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1764935/](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1764935/)

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benkuykendall
Presumably a "species" should be an equivalence class, right? So the relation
"A and B are of the same species" should be transitive, symmetric, and
reflexive. Symmetry is easy (an organism shares 100% of its genome with
itself) as is reflexivity (A shares n% with B iff B shares n% with A).
However, transitivity does not follow obviously: for example, A and B could
share 98%, B and C could share 98%, but A and C could share 96%. Which
species(es) do the three belong to?

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rcthompson
Unfortunately, speciation is mostly a continuous process, so there's no way to
define species by some kind of "degree of similarity/dissimilarity" metric and
have it be a transitive relationship. Any species definition that is
completely transitive will necessarily have edge cases where two extremely
similar organisms fall on different sides of an arbitrary threshold and are
declared to belong to two different species.

The classic example of non-transitive species relationships from sexually
reproducing organisms is a "ring species":
[https://en.wikipedia.org/wiki/Ring_species](https://en.wikipedia.org/wiki/Ring_species)

~~~
sn9
A continuous process and also a human construct that we created to help us
reason about how that continuous process works.

Every biology major learns about the different species concepts/definitions
[0] and why different subfields of biology might prioritize one over another.

[0]
[https://en.wikipedia.org/wiki/Species](https://en.wikipedia.org/wiki/Species)

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kristofferR
Since this wasn't known before, am I right to assume that a lot of giraffes in
zoos are hybrids of the different species?

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sandworm101
They were believed to be sub-species and so I doubt zoos mixed and matched.

The real outcome seems to be that the species is now 1/4 its previous size.
Where there was once one endangered species, now stand four very endangered
species.

Similar and more dramatic story with mantas:
[http://news.nationalgeographic.com/news/2008/07/080731-new-r...](http://news.nationalgeographic.com/news/2008/07/080731-new-
ray.html)

~~~
kristofferR
There's a philosophical question in the fact that something just became more
treasured because of DNA testing results, but I'm not even going to attempt
answering that.

~~~
jacobrobbins
the philosophical questions raised by multiple, visually similar species being
considered as one have come up before. Zebras were discovered to be 3 separate
species. See "What, if anything, is a Zebra?" from 1983
[http://polaris.gseis.ucla.edu/gleazer/462_readings/gould.pdf](http://polaris.gseis.ucla.edu/gleazer/462_readings/gould.pdf)

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dschiptsov
The classic operational definition of different species, as far as I remember,
is that cross-breading between species is not possible.

~~~
openasocket
If only it was! But then we discovered "ring species"
([https://en.wikipedia.org/wiki/Ring_species](https://en.wikipedia.org/wiki/Ring_species))
which threw a monkey wrench into what was once a simple definition. Basically,
there are populations of animals A, B and C, where A and B can inter-breed, B
and C can inter-breed, but A and C can't. So our definition of species no
longer satisfies the transitive property, and it all falls apart. As far as I
know, this issue hasn't yet been satisfactorily answered in the case of ring
species.

~~~
danieltillett
A species is just a human construct to make it easier to understand biological
diversity. In the real world living things are never black and white.

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rrauenza
...except Zebras?

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danieltillett
Even zebras are not black and white - more a dark brown and cream ;)

~~~
J5892
Depends on the camera.

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guessmyname
Off topic — How do I click the links at the bottom of this website?

EDIT: To clarify, as some people thought this was a stupid question... Every
time I scroll down to click one of the links the website scrolls my browser
back up and loads a new article below the one I was reading. I don't want to
read more articles, I want to click the links at the bottom of the website!!!
I was not asking if the links work, they probably do, I am asking how do I
"click them" if the website keeps moving the webview back up when I scroll to
the bottom?

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wodenokoto
they work for me

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guessmyname
How? Every time I scroll down to click one of the links the website scrolls my
browser back up and loads a new article below the one I was reading. I don't
want to read more articles, I want to click the links at the bottom of the
website!!!

I was not asking if the links work, they probably do, I am asking how do I
"click them" if the website keeps moving the webview back up when I scroll to
the bottom?

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nitrogen
Are you talking about the linked site? HN cerainly doesn't do that.

As for infinite scrolling, I am definitely _not_ a fan myself, and this is an
example of why.

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Dylan16807
Infinite scrolling is fine as long as you don't try to also have a footer. And
as long as it's not the only option.

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Myrmornis
A few comments on the academic field that this paper lies in. The aim is to
use DNA sequences to make inferences about the history of the populations.
It's a really vexed area. The core objective is to make statistical inferences
about whether giraffes are one "species" or multiple based on observed DNA
sequences. The core problem is that we can't easily know or approximate the
relevant probability distributions. Compare species-level giraffe taxonomy
with a classification problem in which a large training data set is available,
like determining whether a speech recording is male or female. For speech we
can collect an arbitrarily large training data set. But for giraffes, the
equivalent would be to find a large sample of biological lineages which are in
all other respects like giraffes but differ in that some of them are one
"species" and some multiple, and collect DNA sequences from each of these.
It's fantasy -- it doesn't exist.

To go into a bit more detail: to do the inference task we would need at least
three things:

1\. A definition of "species"

2\. The probability distribution of DNA sequences under the null hypothesis

3\. (For Bayesian approaches) The probability distribution of DNA sequences
under the alternate hypotheses

(1) Is a huge problem because many biologists don't think it's necessary to
worry about the definition. Putting that aside temporarily:

(2). If Giraffes are a single species, what is the probability distribution
from which our observed DNA sequences were sampled? The answer is that it
depends critically on all sorts of other things: social and reproductive
biology of giraffes, giraffe demographics, giraffe post-natal dispersal
patterns. Maybe the most important is that it depends on the geographic
distribution of savanna vegetation types over the past few million years in
sub-saharan Africa. We do not know the effects of any of these on the relevant
probability distributions. The field of population genetics _does_ allow us to
define probability distributions over sampled DNA sequences, but you have to
specify the model. And all the above-listed unknowns and more are relevant to
the model. From a formal statistical point of view you could place priors on
these unknown things and simulate from the marginal distribution of interest,
but in practice that is of course fantasy: there's no convincing way to choose
priors for such things, and there's no way to test it because giraffe
evolution happened once only.

(3). See (2).

The upshot of all this is that while making evolutionary inferences from DNA
sequences is a fascinating discipline, it has some serious challenges and
limitations: we need to recognize that it is not in as happy a place as other
sorts of statistical inferences for which arguments can be made about the
relevant probability distributions needed to make the inference. There is a
huge disconnect between the statistical and theoretical machinery used in the
field, and the ability of practitioners to understand that material. This is
absolutely fair enough: people publishing papers on a particular species are
likely to be ecologists and conservation biologists; but to understand
coalescent theory and the statistical inference techniques used requires
graduate-level understanding of stochastic processes, statistical inference
theory, computational statistics and other stuff from discrete math etc. But
that's not to imply that it would all be fine if people publishing the papers
were professional computational statisticians. The real problem is that while
we wish that we had the ability to make, and more importantly test, these
inferences, the truth is that it's a wildly ambitious inference problem.
Throwing fancy math and computational statistics algorithms at it will get
some people tenure, and will make graduate students in organismal biology feel
intimidated, but it doesn't change that problem.

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dforrestwilson1
So is Pluto a planet or not then?

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bfuller
Giraffes? Giraffes!

