Does "Species" Mean What It Used To ? New Data = New Thinking

[Mr. B1ack]

When all we could do was kind-of LOOK a things,
maybe poke around a bit in their gooey insides, we
subdivided life into certain distinct species.

When we could finally read the DNA sequences we
found we'd made some mistakes ... looks don't tell the
whole story.

Now we discover that exogentic factors heavily
regulate what genes are 'on' or 'off' - and that
adds a whole new layer of complexity and
potential interactions.

So ... how many "species" really AREN'T "species"
at all, but essentially the same basic DNA library
simply sub-sampled by methylation "switches" ?
Are Darwins finches REALLY different species
or just variations on the theme - like Great Danes
and weiner-dogs ?

New knowledge sometimes requires new paradigms
and it's probably time to seriously re-think the word
"species" ... or maybe dump it entirely.

[RSNorman]

Post by Mr. B1ack
When all we could do was kind-of LOOK a things,
maybe poke around a bit in their gooey insides, we
subdivided life into certain distinct species.
When we could finally read the DNA sequences we
found we'd made some mistakes ... looks don't tell the
whole story.
Now we discover that exogentic factors heavily
regulate what genes are 'on' or 'off' - and that
adds a whole new layer of complexity and
potential interactions.
So ... how many "species" really AREN'T "species"
at all, but essentially the same basic DNA library
simply sub-sampled by methylation "switches" ?
Are Darwins finches REALLY different species
or just variations on the theme - like Great Danes
and weiner-dogs ?
New knowledge sometimes requires new paradigms
and it's probably time to seriously re-think the word
"species" ... or maybe dump it entirely.

You suggest an interesting idea that conceptually could be true.
However what we do know about epigenetic factors so far is that,
although they can be inherited across perhaps a few generations, they
simply do not persist over the time spans the distinguish species.

The specific case you mention, Darwin Finches, is known. The paper
"Evolution of Darwin’s finches and their beaks revealed by genome
sequencing" says: "we report the results of whole-genome re-sequencing
of 120 individuals representing all of the Darwin’s finch species and
two close relatives. Phylogenetic analysis reveals important
discrepancies with the phenotype-based taxonomy. We find extensive
evidence for interspecific gene flow throughout the radiation.
Hybridization has given rise to species of mixed ancestry."
http://www.nature.com/nature/journal/v518/n7539/full/nature14181.html

We already know that the species boundary in general is somewhat
porous and that hybridization occurs commonly in nature. We do
occasionally revise our notion of species as "varieties" or
"varieties" as true species, processes informally called "lumping" and
"splitting". But nothing we have seen so far indicates that
epigenetics rises to the level of redefining the notion of species.

Beyond that, even if epigenetic patterns were persistent and separated
types, it would not influence the biological concept of species. If
two populations are reproductively isolated, no matter the reason for
the isolation or the details of the difference, they constitute
different species. If they readily hybridize to the extent of
essentially sharing one common gene pool, then they are not. Even the
definition of evolution as a change in the genetic composition of a
population can included as "genetic" all factors that are inherited
through the reproductive process including epigenetic factors.

[Ernest Major]

Post by Mr. B1ack
When all we could do was kind-of LOOK a things,
maybe poke around a bit in their gooey insides, we
subdivided life into certain distinct species.
When we could finally read the DNA sequences we
found we'd made some mistakes ... looks don't tell the
whole story.

That is true, but the mistakes that have been found are generally in the
opposite direction to that you suggest - two or more similar looking
species being mistaken for a single species.

Post by Mr. B1ack
Now we discover that exogentic factors heavily
regulate what genes are 'on' or 'off' - and that
adds a whole new layer of complexity and
potential interactions.

The word you are looking for is epigenetic.

Post by Mr. B1ack
So ... how many "species" really AREN'T "species"
at all, but essentially the same basic DNA library
simply sub-sampled by methylation "switches" ?
Are Darwins finches REALLY different species
or just variations on the theme - like Great Danes
and weiner-dogs ?

If your hypothesis was correct we would be finding groups of closely
related species with the diversity of the whole group showing comparable
genetic diversity to domestic dogs. I would be surprised if this has
been happening without me noticing it.

Post by Mr. B1ack
New knowledge sometimes requires new paradigms
and it's probably time to seriously re-think the word
"species" ... or maybe dump it entirely.

There are cases where methylation patterns result in different looking
individuals - in sexually dimorphic species (e.g. angler fish), in
species that undergo metamorphosis during development (e.g. caterpillar
vs. butterfly, elver vs. eel), in social insects, the solitary and
migratory phases of the locust, or the solitary and colonial phases of
slime moulds. Mistaking two forms of a species for two species has been
quite rare, though it did happen for some eels. Nowadays it is
recognised that larval eels are not a different species from the adults,
but it might require DNA sequencing to work out which larval form goes
with which adult form.

Methylation patterns mostly depend on the genome and are reset during
reproduction; no-one has yet found a difference in methylation patterns
persisting over more than a few generations.

If we did find two populations which had the same genome, but a
persistent difference in methylation patterns and appearance then if
they were reproductively isolated they would still be considered
different species (per the BSC). If they weren't reproductively isolated
then it's unlikely that a difference in methylation patterns would persist.

[Mike Duffy]

Post by Mr. B1ack
and it's probably time to seriously re-think the word
"species" ... or maybe dump it entirely.

How about "kind"?

[Mr. B1ack]

Post by Mike Duffy

Post by Mr. B1ack
and it's probably time to seriously re-think the word
"species" ... or maybe dump it entirely.

How about "kind"?

Hmm ... maybe a little TOO broad and imprecise.

"Species" still has merit IF we can better pin down
what it's supposed to mean in light of our new
bounty of knowledge.

My concern is that epigenetics has created a lot
of effectively "false species" that kind of LOOK
different but, when you get down to the brass tacks,
really aren't different enough to warrant a "species"
label.

I used dogs as an example. Here we've had deliberate
high-pressure selection for phenotype resulting in
animals no naive person would ever believe weren't
of entirely different species. Alas, the "difference" is
all epigenetic, all dogs are (aside from mechanical
factors) capable of breeding with all others ... no real
genetic differences worth a damn. Crossbreed for
just a few generations and you get your basic yellow
cur again - they're all over many big cities - the
epigentic markers blend back to "average".

[Ernest Major]

Post by Mr. B1ack

Post by Mike Duffy

Post by Mr. B1ack
and it's probably time to seriously re-think the word
"species" ... or maybe dump it entirely.

How about "kind"?

Hmm ... maybe a little TOO broad and imprecise.
"Species" still has merit IF we can better pin down
what it's supposed to mean in light of our new
bounty of knowledge.
My concern is that epigenetics has created a lot
of effectively "false species" that kind of LOOK
different but, when you get down to the brass tacks,
really aren't different enough to warrant a "species"
label.
I used dogs as an example. Here we've had deliberate
high-pressure selection for phenotype resulting in
animals no naive person would ever believe weren't
of entirely different species. Alas, the "difference" is
all epigenetic, all dogs are (aside from mechanical
factors) capable of breeding with all others ... no real
genetic differences worth a damn. Crossbreed for
just a few generations and you get your basic yellow
cur again - they're all over many big cities - the
epigentic markers blend back to "average".

That is not my understanding. Can you provide any citations for the
claim that the differences between dog breeds are epigenetic rather than
genetic.

[RSNorman]

Post by Mr. B1ack

Post by Mike Duffy

Post by Mr. B1ack
and it's probably time to seriously re-think the word
"species" ... or maybe dump it entirely.

How about "kind"?

Hmm ... maybe a little TOO broad and imprecise.
"Species" still has merit IF we can better pin down
what it's supposed to mean in light of our new
bounty of knowledge.
My concern is that epigenetics has created a lot
of effectively "false species" that kind of LOOK
different but, when you get down to the brass tacks,
really aren't different enough to warrant a "species"
label.
I used dogs as an example. Here we've had deliberate
high-pressure selection for phenotype resulting in
animals no naive person would ever believe weren't
of entirely different species. Alas, the "difference" is
all epigenetic, all dogs are (aside from mechanical
factors) capable of breeding with all others ... no real
genetic differences worth a damn. Crossbreed for
just a few generations and you get your basic yellow
cur again - they're all over many big cities - the
epigentic markers blend back to "average".

Apparently you do not read too well. I already said that your idea
had some conceptual merit but absolutely everything we have seen about
species including doing an awful lot of genetic analysis and
everything we know about the mechanisms of epigenetics says that it
cannot work the way you suggest.

You confuse epigenetic markers for stages of a life cycle or
epigenetic markers for sexual dimorphism or epigenetic markers for
castes of social insects with races or subspecies or breeds. One
lasts at most the lifetime of one individual; the other perpetuates
indefinitely through generations of reproduction.