Jim LeNomenclatoriste
Je suis un mignon petit Traquet rubicole
No the Woodcocks
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Taxonomy in-flux updates (2 Viewers)
- Thread starter Mysticete
- Start date
l_raty
laurent raty
The dowitchers, I think.
Jim LeNomenclatoriste
Je suis un mignon petit Traquet rubicole
The main tree in the paper shows Lymnocryptes close to Scolopax
l_raty
laurent raty
Not based on the paper.
There is a lot of data, including a complete genome of Lymnocryptes, in Genbank which were not used in the paper.
Jim LeNomenclatoriste
Je suis un mignon petit Traquet rubicole
What do the other results say?
You would be able to recreate the entire tree of Charadriiformes at generic level?
l_raty
laurent raty
Probably, but not overnight...
johnallcock
Well-known member
This is mentioned in the TiF page: TiF Checklist: GRUAE II: Charadriiformes
Apparently the chimera in an earlier version of the paper has now been corrected and the revised sequence places Lymnocryptes with the dowitchers genetically, but the paper groups it with woodcocks for morphological reasons.
Interestingly, the species tree in the paper suggests the split between Asian Dowitcher and Long/Short-billed is very old (older even than the split between snipes and woodcocks). Given this and the morphological distinctiveness of Asian Dowitcher, it seems sensible to me that these could be treated as different genera.
l_raty
laurent raty
A large chunk (> 1000 bp) of the old RAG1 sequence of Lymnocryptes was 100% identical to that of Limosa haemastica, and ended up phylogenetically where this species was expected.
I've attached a quick-and-dirty ML tree built from RAG1 sequences of Scolopacidae. The sequences with a standard accession number (2 letters-6 figures) are in the GenBank nucleotide database as RAG1 sequences; those with a longer accession number (most often 6 letters-9 figures) were retrieved from scaffolds of whole genome shotgun sequences using BLAST. (I coloured in red a couple of sequences that seemed readily and obviously problematic, among which the Lymnocryptes sequence in question. Look where the other sequence ends up.)
l_raty
laurent raty
This would be Pseudoscolopax Blyth 1859.
Jim LeNomenclatoriste
Je suis un mignon petit Traquet rubicole
I have been using this genus for semipalmatus for a long time but I did not imagine that Lymnocryptes was paraphyletic with Limnodromus (lato sensu). Is there another topology where Lymnocryptes would be sister to Limnodromus+Pseudoscolopax?
Is this paraphyly strongly supported?
l_raty
laurent raty
Snapdragyn
Well-known member
Ah, that it explains it. I only found the early version of the paper online, so I was looking at the tree that used the chimaera sequence (& subsequent placement).
Jim LeNomenclatoriste
Je suis un mignon petit Traquet rubicole
I'm interested in knowing if I should combine these three genrera under the same common name or if I leave them as Bécassin and Bécassette. Besides, I would like to know the origin of the name Bécassin but that is another story.I can't answer that without a lot more work.
James Jobling
Well-known member
Jim,
Bécasse, Bécasseau, Bécassin and Bécassine are all explained in Cabard, 2022, L’étymologie des noms d’oiseaux, Nouvelle édition révisée, pp. 216-221, but I couldn’t find Bécassette there.
Bécasse, Bécasseau, Bécassin and Bécassine are all explained in Cabard, 2022, L’étymologie des noms d’oiseaux, Nouvelle édition révisée, pp. 216-221, but I couldn’t find Bécassette there.
Jim LeNomenclatoriste
Je suis un mignon petit Traquet rubicole
Bécassette is my creation for my French nomenclature of birds😉
James Jobling
Well-known member
I like Becassette. If only we could create new English names without WWIII breaking out!
Jim LeNomenclatoriste
Je suis un mignon petit Traquet rubicole
December 2024
December 21
Dowitchers: The split between the Asian Dowitcher and the two American dowitchers looks pretty old in Černý and Natale (2022). In fact, figure 6 shows it at about 29 mya, too old for all the dowitchers to be in the same genus. Rescaling using Stiller et al. (2024) dates reduces the age of the dowitcher split, but it is still old, around 22 mya. That's way too old for all three species to be in the same genus. As a result, I moved the Asian Dowitcher to the monotypic genus Pseudoscolopax Blyth, 1859. The Asian Dowitcher is now Pseudoscolopax semipalmatus.
Jack Snipe: We still aren't sure where the Jack Snipe fits it. According to Černý and Natale (2022), DNA embeds it in the dowitchers. Morphology puts it sister to the snipe-woodcock clade, and their total evidence tree (fig. 6) has it a distant relative of the woodcocks. Dufour et al. (2024), using DNA only, have it as basal in Scolopacinae. I've put it sister to the snipe-woodcock clade, but have little confidence in this.
Snipe: The Noble Snipe wasn't originally part of Chubbia, and I think it was a mistake on my part to move it there (I think I just carried it along when I moved Chubbia). I'm returning the Noble Snipe to genus Gallinago, and putting it next to the Puna, Pantanal, Magellanic Snipe (G. andina, paraguaiae, and magellanica). Without genetic data on it, I'm reluctant to assume it is their sister taxon.
It may turn out that the Giant Snipe belongs in Chubbia, but it may not. It looks different, and the RAG-1 evidence also suggests it is not. Because of this, I've placed it in Xylocota, Bonaparte 1839 (the name belongs to the nominate subspecies). The name Homoptilura, G.R. Gray 1840 has also been applied to the Giant Snipe. In fact, both names are based on Buffon's illustration of the type. Since Bonaparte's name was proposed first, it gets the nod. It's rather easy to see the illustration is of a Giant Snipe.
Finally, the two remaining Chubbia are placed sister to the Imperial Snipe, which has generally been considered the third member of the Chubbia group. It looks different enough that I've removed it it from Chubbia. The quesion marks in the tree indicate I'm not where the two remaining Chubbia belong.
Also, I'd like thank BirdForum members for the helpful comments they posted.
[Charadriiformes, Scolopacidae, 3.51]
What figure is he referring to when he talks about Dufour (2024)?
December 21
Dowitchers: The split between the Asian Dowitcher and the two American dowitchers looks pretty old in Černý and Natale (2022). In fact, figure 6 shows it at about 29 mya, too old for all the dowitchers to be in the same genus. Rescaling using Stiller et al. (2024) dates reduces the age of the dowitcher split, but it is still old, around 22 mya. That's way too old for all three species to be in the same genus. As a result, I moved the Asian Dowitcher to the monotypic genus Pseudoscolopax Blyth, 1859. The Asian Dowitcher is now Pseudoscolopax semipalmatus.
Jack Snipe: We still aren't sure where the Jack Snipe fits it. According to Černý and Natale (2022), DNA embeds it in the dowitchers. Morphology puts it sister to the snipe-woodcock clade, and their total evidence tree (fig. 6) has it a distant relative of the woodcocks. Dufour et al. (2024), using DNA only, have it as basal in Scolopacinae. I've put it sister to the snipe-woodcock clade, but have little confidence in this.
Snipe: The Noble Snipe wasn't originally part of Chubbia, and I think it was a mistake on my part to move it there (I think I just carried it along when I moved Chubbia). I'm returning the Noble Snipe to genus Gallinago, and putting it next to the Puna, Pantanal, Magellanic Snipe (G. andina, paraguaiae, and magellanica). Without genetic data on it, I'm reluctant to assume it is their sister taxon.
It may turn out that the Giant Snipe belongs in Chubbia, but it may not. It looks different, and the RAG-1 evidence also suggests it is not. Because of this, I've placed it in Xylocota, Bonaparte 1839 (the name belongs to the nominate subspecies). The name Homoptilura, G.R. Gray 1840 has also been applied to the Giant Snipe. In fact, both names are based on Buffon's illustration of the type. Since Bonaparte's name was proposed first, it gets the nod. It's rather easy to see the illustration is of a Giant Snipe.
Finally, the two remaining Chubbia are placed sister to the Imperial Snipe, which has generally been considered the third member of the Chubbia group. It looks different enough that I've removed it it from Chubbia. The quesion marks in the tree indicate I'm not where the two remaining Chubbia belong.
Also, I'd like thank BirdForum members for the helpful comments they posted.
[Charadriiformes, Scolopacidae, 3.51]
What figure is he referring to when he talks about Dufour (2024)?
l_raty
laurent raty
Fig. S1. (In the "supporting information" file.)
Jim LeNomenclatoriste
Je suis un mignon petit Traquet rubicole
December 25
Caracaras: Fuch et al. (2015) found that many of the caracaras are closely related, with their living with their common ancestor estimated to live less than 5 million years ago. The differences between them are not large, so I've merged the genera Ibycter, Milvago, and Phalcoboenus into Daptrius. See also SACC proposal #1038.
[Falconidae, Basal Australaves, 3.49a]
This is the better choice
Caracaras: Fuch et al. (2015) found that many of the caracaras are closely related, with their living with their common ancestor estimated to live less than 5 million years ago. The differences between them are not large, so I've merged the genera Ibycter, Milvago, and Phalcoboenus into Daptrius. See also SACC proposal #1038.
[Falconidae, Basal Australaves, 3.49a]
This is the better choice
