Jim LeNomenclatoriste
Je suis un mignon petit Traquet rubicole
So, two species minimum would be best for now 🤔
Last edited:
-
Welcome to BirdForum, the internet's largest birding community with thousands of members from all over the world. The forums are dedicated to wild birds, birding, binoculars and equipment and all that goes with it.
Please register for an account to take part in the discussions in the forum, post your pictures in the gallery and more.
Ardeidae (1 Viewer)
- Thread starter Richard Klim
- Start date
Peter Boesman
Well-known member
See also my note on vocal differences between Great Egret taxa:
Birds of the World
In summary, it supports a species-level split of egretta from the New World, a conclusion also reached by Pratt 2011 based on different arguments.
Birds of the World
In summary, it supports a species-level split of egretta from the New World, a conclusion also reached by Pratt 2011 based on different arguments.
Jim LeNomenclatoriste
Je suis un mignon petit Traquet rubicole
I ask this because I was reading the descriptions of this species made by old French naturalist authors (Buffon & Cie) and I noticed something that could imply quite a lot about the French names of these taxa (alba and egretta) if a split came. Things that don't concern English speakers naturally.
l_raty
laurent raty
The cox1 distance between alba (n=8, Sweden, Germany, Austria, Japan) and egretta (n=12, Argentina, Suriname, Salvador, Mexico, USA) is 2.4%.
The cox1 distance between Asian (in BOLD: n=13, S Korea, Japan; additional seqs in GenBank: n=6, China, India) and Australian (n=1) modesta is about 2%.
The cox1 distance between modesta and the [alba + egretta] clade is 4.2-5.2%.
For comparison, the cox1 distances between species in the Ardea cinerea / herodias / cocoi complex are 1.3-1.4%.
The cox1 distance between Asian (in BOLD: n=13, S Korea, Japan; additional seqs in GenBank: n=6, China, India) and Australian (n=1) modesta is about 2%.
The cox1 distance between modesta and the [alba + egretta] clade is 4.2-5.2%.
For comparison, the cox1 distances between species in the Ardea cinerea / herodias / cocoi complex are 1.3-1.4%.
Jim LeNomenclatoriste
Je suis un mignon petit Traquet rubicole
l_raty
laurent raty
Part of the BOLD data cannot be downloaded (you can only see the stats for each BIN -- for ex., in the A. a. alba BIN, the German and Austrian sequences are not public; but you can see a haplotype network for the whole BIN where they appear, hence you can be completely sure that they are like the public Swedish sequence).
I have attached a quick and dirty tree built from public sequences of Ardea (sensu lato), rooted with two sequences of Butorides and Ardeola.
(I tried to remove duplicates (seqs found under two accession numbers in GenBank, or both in GenBank and in BOLD), but I wouldn't exclude the possibility that a few remain.)
Jim LeNomenclatoriste
Je suis un mignon petit Traquet rubicole
There are not data for melanorhynchos ?
l_raty
laurent raty
No, sorry.
No sequences of Intermediate Egrets from elsewhere than Asia, either. (There is one sequence labelled intermedia from Australia in BOLD, but it seems to be a misidentified Eastern Cattle Egret.)
Last edited:
Peter Boesman
Well-known member
The paper below presumably includes a bird from South Africa brachyrhyncha.
I don't have access to the paper , so I can't verify if that's correct...
Hruska, J. P., J. Holmes, C. Oliveros, S. Shakya, P. Lavretsky, K. G. McCracken, F. H. Sheldon, and R. G. Moyle (2023). Ultraconserved elements resolve the phylogeny and corrobrate patterns of molecular rate variation in herons (Aves: Ardeidae). Ornithology 140(2):1-21
l_raty
laurent raty
Yes, correct, and they did recover mtDNA sequences, albeit not for all the species they studied.
(Their data are neither in GenBank, nor in BOLD, but deposited on Dryad -- you have to know they're there to find them.)
I extracted the barcode region of Ardea spp from their alignments and added these to the data set to build a new tree.
The uncorrected distance between nominate intermedia and brachyrhyncha for this region (and based on a single sequence for brachyrhyncha) is about 4.6%.
Last edited:
Jim LeNomenclatoriste
Je suis un mignon petit Traquet rubicole
The only unknowns in Ardeidae are Ardea sumatrana and Egretta picata
Obviously, they put their file in formats that cannot be opened !!!!!
Last edited:
l_raty
laurent raty
They deposited the data set as a .tar.gz file, but Dryad compresses it once more into a .zip before it lets you download it...
(I had no real problem with it... Downloading 948 Mb to get 7 barcodes (~50 kb of info) felt a bit extreme, though.
)
Last edited:
Jim LeNomenclatoriste
Je suis un mignon petit Traquet rubicole
Files are in .md and .gz format after extractionThey deposited the data set as a .tar.gz file, but Dryad compresses it once more into a .zip before it lets you download it...
(I had no real problem with it... Downloading 948 Mb to get 7 barcodes (~50 kb of info) may be a bit extreme, though.
Jim LeNomenclatoriste
Je suis un mignon petit Traquet rubicole
How to do, i don't have the tool?
Do you have 7-zip? It can deal with these. Or just Google for other free options
Jim LeNomenclatoriste
Je suis un mignon petit Traquet rubicole
No 😐 could you do it for me plz ? 😏
Peter Boesman
Well-known member
Thanks Laurent for the detective work ! And the genetic tree provides great info.
It would seem that there are about similar arguments for splitting Intermediate Egret and Great Egret: Considerable genetic distance, morphological differences and some vocal differences. Relatively strong cases I would think (with still some genetic data lacking here and there).
In the case of Great Egret, a split into 3 (rather than 2) species seems the better approach when integrating all arguments.
(Unless there would be clear morphological or vocal differences, a further split of the Australian birds seems premature)
I guess you could send me a pm. But really, you do need to get a tool yourself. This kind of archive is commonplace.
l_raty
laurent raty
The uncompressed data includes close to 5,000 files, for a total of about 4 Gb, it's not something that can be attached to an email.
If you have a relatively recent version of Windows (I assume you use Windows, otherwise the problem would not even occur), it seems you should be able to extract .tar.gz files without installing third-party software, using the command line -- see the first procedure described here. (I don't have a computer running Windows at hand to test if this really works, though.)
Most of it is genetic sequences (.phylip, .nex, .fasta files) and individual gene trees (.tre files). Can I ask what you want to do with it, exactly ? Is there a part of it in which you would be particularly interested ?
If you have a relatively recent version of Windows (I assume you use Windows, otherwise the problem would not even occur), it seems you should be able to extract .tar.gz files without installing third-party software, using the command line -- see the first procedure described here. (I don't have a computer running Windows at hand to test if this really works, though.)
Most of it is genetic sequences (.phylip, .nex, .fasta files) and individual gene trees (.tre files). Can I ask what you want to do with it, exactly ? Is there a part of it in which you would be particularly interested ?
Last edited:
