DNA Barcoding

[Chriswilko]

This deserves discussion...... Multiple 'Winter' Wren species I can accept as well as Arctic and Common Redpolls being lumped. Not sure about the Gulls though and how can Cinnamon and Blue Winged Teals be 100% similar? There must be something in the DNA somewhere that results in their different morpholgy....

The article:

Today two papers on "DNA barcoding" of birds and bats were published in the journal Molecular Ecology Notes. These papers describe recent work done on species of North American birds and Guyanese bats using the DNA barcoding technique to explore existing taxonomy. They reveal a number of interesting results, including the discovery of previously unknown species which has implications on our assessment of biodiversity (click here for the detailed press releases).

Scientists have successfully tested their ability to identify and DNA barcode entire families of species - the prelude to a genetic portrait of all animal life on Earth. The Barcode of Life project now has more than 25,000 species of animal catalogued and scientists hope to increase this to 500,000 species by 2014. Based on work undertaken so far, they have announced the discovery of 15 new genetically distinct species of bird. Don't reach for those armchair ticks just yet though: those identified are nearly indistinguishable to human eyes and ears. They have been "overlooked" through centuries of bird study, and attention to the minutiae of various feather tracts is unlikely to lead modern birders to be able to separate them confidently either!

"Overlooked species", where DNA barcoding reveals genetically divergent lineages signalling the probable presence of different species, of interest to European birders include:

Fulmar
Solitary Sandpiper
Common Raven
Wren
Hermit Thrush
The authors reveal more news of interest for European birders. Not only do we have the prospect of species that we're unable to tell apart, but the authors of the present studies also propose that some species that we consider to be "good' species in their own right have virtually identical DNA. These include:

Snow Goose and Ross's Goose (99.8% similarity)
Black Duck, Mallard and Mottled Duck (99.4 % similarity)
Blue-winged Teal and Cinnamon Teal (100% similarity)
King Eider and Eider (99.7 % similarity)
Laughing Gull and Franklin's Gull (99.3 % similarity)
California Gull, Herring Gull, Thayer's Gull, Iceland Gull, Lesser Black-backed Gull, Western Gull, Glaucous-winged Gull and Glaucous Gull (99.8 % similarity)
Common Redpoll and Arctic Redpoll of the race hornemanni (99.7 % similarity)

[Xenospiza]

There really aren't that many surprises in the article (if you followed the literature). The press release for the article presents things in an overly simplified way – which of course works like a charm (meaning: it's picked up by journalists, unlike more thorough work that does not present its findings so bluntly).

They are mixing up "clades" and "species" (the DNA shows basically the history of a taxon, not the present state).
For the Raven situation, there is a recent review article in Dutch Birding.
The Winter Wren could (I'd say: should) be split into (at least) three species, possibly more if Eurasia is sampled more.
Carolina Chickadee (which I miss here) consists of two very different clades (east and west) that mix freely where they meet: the same is true for Mountain Chickadee.
Many gulls and ducks have very recent origins (hence virtually similar DNA profiles), but here visual and auditory signals obviously work well to separate them (most of the time).

I think the barcoding work is an interesting onset for further research in a few cases (Solitary Sandpiper is one), but in many cases I'm underwhelmed by what is presented as spectacular news in the press release.

[jurek]

These DNA barcodes were already presented 2-3 years ago. They were later rebuked as distracting from "real" work.

Similarity of gulls and redpolls at least was alredy known from other DNA studies.

[Chriswilko]

Does anybody know the origin of the oft quoted figure of 2.5% divergance to define a 'good' species. This seems the most arbitary definition of all.

[njlarsen]

Does anybody know the origin of the oft quoted figure of 2.5% divergance to define a 'good' species. This seems the most arbitary definition of all.

I don't know the origin, and I don't think the number is of global value. I have a paper at home quoting about 2% for separating most good species of owls; at one time, I think heard a talk stating that the number needs to be calibrated within each family one works with.

The DNA Barr-code proponents have chosen a relatively short piece of mitochondrial genome to work on. That can be good as an initial tool to identify intersting problems, but I would personally prefer to see a longer DNA sequence used for further work on these problems, and if possible, some comparison that included the rest of the genome. The latter is much more difficult to work on, as the sequence differences develop much more slowly.

Niels

[Stephen Menzie]

how can Cinnamon and Blue Winged Teals be 100% similar? There must be something in the DNA somewhere that results in their different morpholgy....


The phenotype of an organism (what you see 'on the outside') is down to expression of genes, not the presence of genes. Some genes can be suppressed or not activated and therefore their effect on the organism will never be seen. Different genes are activated/suppressed in different species (e.g. B-w and Cinnamon Teal).
However, I suspect (although I haven't read the press release) that most of this work will have been done on mtDNA (from in the mitochondria of the cell, not the DNA from within the nucleus that everyone thinks of). As Xeno said, this is only going to give a idea of the time since the species diverged - 100% similarity means that in evolutionary terms the species only 'formed' very recently. The larger the p.c. difference, the longer the time since the species were one and the same. mtDNA is going to play very little, if any part in phenotypic expression in the animal and this would explain why the results suggest that several species should look the same but in reality look quite different!

Stephen :gn:

[jurek]

Blue-winged Teal and Cinnamon Teal (100% similarity)
King Eider and Eider (99.7 % similarity)
Laughing Gull and Franklin's Gull (99.3 % similarity)
California Gull, Herring Gull, Thayer's Gull, Iceland Gull, Lesser Black-backed Gull, Western Gull, Glaucous-winged Gull and Glaucous Gull (99.8 % similarity)


I would say simply - "DNA barcodes method" was shown to be failure in recognizing species. So just forget it as a wrong method for the purpose.

[birderbf]

[QUOTE]
California Gull, Herring Gull, Thayer's Gull, Iceland Gull, Lesser Black-backed Gull, Western Gull, Glaucous-winged Gull and Glaucous Gull (99.8 % similarity)
[QUOTE]

OK, if they can't surely separate Glaucous-winged Gulls out west, where the breed with Western, maybe Herring and Thayer's, how in the world can they prove the recent British Glaucous-winged Gull to be what it was?

[AlexC]

OK, if they can't surely separate Glaucous-winged Gulls out west, where the breed with Western, maybe Herring and Thayer's, how in the world can they prove the recent British Glaucous-winged Gull to be what it was?

That's the point (EDIT: that this thread is making) - they can - DNA Barcoding is just not accurate when it comes to separating species.

[Gentoo]

California Gull, Herring Gull, Thayer's Gull, Iceland Gull, Lesser Black-backed Gull, Western Gull, Glaucous-winged Gull and Glaucous Gull (99.8 % similarity)Where do Kelp, Great Black-Backed and Yellow-Footed Gulls fit into this? From other things I've read, they too are supposed to be very close to all the afforementioned speices.

Eactly how many Winter Wrens are they thinking of?

[AlexC]

Where do Kelp, Great Black-Backed and Yellow-Footed Gulls fit into this? From other things I've read, they too are supposed to be very close to all the afforementioned speices.

Eactly how many Winter Wrens are they thinking of?

I remember reading it was all large white-headed gulls that were, in this study, found to be very close, so I think they fit right in with that.

[Xenospiza]

Where do Kelp, Great Black-Backed and Yellow-Footed Gulls fit into this? From other things I've read, they too are supposed to be very close to all the afforementioned speices.

Eactly how many Winter Wrens are they thinking of?
You can think of Eastern ("Taiga") Winter Wren, Pacific Winter Wren and any number from one to four Palearctic Winter Wrens (though I think there is not enough sampling to justify any conclusions yet, and I don't know how much their songs vary – one would suit me fine).

[Gentoo]

You can think of Eastern ("Taiga") Winter Wren, Pacific Winter Wren and any number from one to four Palearctic Winter Wrens (though I think there is not enough sampling to justify any conclusions yet, and I don't know how much their songs vary – one would suit me fine).
I know there are slight variations in songs with Western Birds teding to be more prolonged and it seems a bit quicker. I'm only judging off of recordings I've heard of eastern birds and both recordings and real life examples of western.

I can see them making a split like that too as well as perhaps resplitting some of the House wrens.