DNA barcoding: According to their kinds


(Martin R) #1

Hey everybody.

i am new here, but i already met some of you.

Recently i came across an article on DNA barcoding.

My English is bad (i am not native), and perhaps i misunderstood something…

So, is it true, that 90% of animals have an UNIQUE 600bp DNA sequence in their mitochondrial genome?

From what i could understand, this relatively short DNA sequence (COI) is what the DNA barcoding is based on. DNA barcoding is used by scientists and also in everyday life to identify species (e.g. what kind of meat is in your hamburger). At this moment there are 100,000 species in DNA barcode database (and counting)

It looks like the Bible was right “And God made the beasts of the earth according to their kinds…”, moreover, it seems like our Creator put a barcode on each of it…


An engineer asks: Who understands evolution?
(Stephen Matheson) #2

That’s roughly correct. You can read more at the Barcode of Life project site:

http://ibol.org/phase1/about-us/what-is-dna-barcoding/


(Martin R) #3

thanks for a prompt reply.

So how that happened ? (if you consider it is a mitochondrial genome… a very fragile thing)

Is there any theory, hypothesis or a speculation?


(Steve Schaffner) #4

It happened the usual way: the accumulation of mutations since the species last shared a common ancestor. DNA sequence usually differs between species.


(Stephen Matheson) #5

I don’t know why you think the mito genome is a “very fragile thing” or why this would matter for COI barcoding. (It doesn’t.)

Your question “how did this happen?” seems to presume that the existence of unique sequences in COI is remarkable. I’m not sure that it is. My understanding of the COI barcode is that it was chosen by humans based on the fact that it is ubiquitous because COI is a basic gene required in all living things (that have mitochondria, which of course excludes the vast majority of Earth’s living things, but that’s not important here). The 600-bp region is easy to amplify by PCR, and that was a key technical aspect when species barcoding was first proposed 15 years ago. I think that the gene was already known to exhibit substantial diversity between species. In other words, at first glance, the COI barcode is just a convenient way to look at species-specific DNA sequences for identification purposes. The existence of species-specific DNA sequences by itself is not surprising or interesting, and requires no special explanation other than some measure of reproductive isolation and, of course, common descent from some founding population.

However, I just looked at a recent paper that argues that COI is a particularly good choice, because it is biologically relevant to speciation itself. That is cool and interesting, because speciation genes are cool and interesting, and it seems to imply that the COI barcode was a great idea. But if you read the paper, you’ll see that there is debate and uncertainty surrounding COI as a barcode. I think this is unsurprising, simply because biology and population genetics can be a little too complicated for something as simple as a “barcode” for a species. It’s a great idea, and a useful tool, but not a singular proof or something like that.


(Martin R) #6

hm… i always thought that common ancestry is based on DNA sequence similarities…


(Stephen Matheson) #7

Wow, then you should read a lot more. There are great resources right here on BL about basic scientific concepts like common ancestry and DNA sequences.


(Martin R) #8

Hm… that is weird, so those 200,000 ERV insertions are not similar DNA sequences across the apes-species?


(Stephen Matheson) #9

If you think that “common ancestry is based on DNA sequence similarities” alone, then you haven’t read the most basic facts about phylogenetics. Which makes discussion with you on that topic pointless.


(Martin R) #10

yes, indeed… it seems to be remarkable…

i am not the only one who is wondering:

“What evolutionary mechanisms account for synonymous clusters being largely coincident with species?”


(Martin R) #12

alright, so now you admit that common ancestry is based on DNA sequence similarities … that is what i said before. So why we are still talking about common ancestry?


(Stephen Matheson) #13

Nice article, thanks for sharing it! It was very interesting.

But you have misunderstood it. The authors are not trying to understand why there are species-specific DNA sequences. That’s not interesting at all, by itself. They are trying to understand why mitochondria, in particular, seem to track with species and speciation. This is what I already mentioned as interesting, in a post above.


(Stephen Matheson) #14

I can’t tell whether you are intentionally distorting what I write, or whether you just can’t understand me. I think that either one means there is no point in continuing.


(Martin R) #15

ok, so again, from that article:

“What evolutionary mechanisms account for synonymous clusters being largely coincident with species?”


(Martin R) #16

“New work by a pioneering scientist details how subtle changes in mitochondrial function may cause a broad range of common metabolic and degenerative diseases.”

“The discrete changes in nuclear gene expression in response to small increases in mitochondrial DNA mutant level are analogous to the phase changes that result from adding heat to ice,” said Wallace. “As heat is added, the ice abruptly turns to water and with more heat, the water turns abruptly to steam.” Here a quantitative change (an increasing proportion of mitochondrial DNA mutation) results in a qualitative change (coordinate changes in nuclear gene expression together with discrete changes in clinical symptoms)."

https://www.chop.edu/news/steadily-rising-increases-mitochondrial-dna-mutations-cause-abrupt-shifts-disease


(Stephen Matheson) #17

That article isn’t about mito genome fragility, and the quotes you provide don’t have anything at all to do with mito genome fragility. Wouldn’t it be better to learn more before posting all this stuff? Just a thought.


(Martin R) #18

“New work by a pioneering scientist details how subtle changes in mitochondrial function may cause a broad range of common metabolic and degenerative diseases.”

"…subtle changes… may cause a broad range of common metabolic and degenerative diseases… "

why is it wrong to say that mitochondrial genome is very fragile? What is wrong with that? Could you be more specific?


(Martin R) #19

please don’t teach me lessons… why don’t you answer the main question? let me repeat:

“What evolutionary mechanisms account for synonymous clusters being largely coincident with species?”


(Haywood Clark) #20

Aren’t you asking for a lesson with your question?

Have you considered reading material in your native language before misinterpreting English material?


#21

That means small changes.

Fragile means easily broken. Not the same thing.

If the mitochondrial genome was really fragile (easily broken) I don’t think life that is based on mitochondria would have survived this long. Small changes, when they do occur, can have a big impact.