• 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.
ZEISS DTI thermal imaging cameras. For more discoveries at night, and during the day.

Gruiformes and Charadriiformes (1 Viewer)

No, I didn't find what I was looking for, although skimming through the paper I did manage to answer my own questions and on some TiF decisions.

Random comments:

Not sure I feel comfortable splitting apart Calidris. While in theory I don't mind cryptic genera, to me the degree of morphological similarity makes me question the merit of finely splitting apart the genus as currently recognized. I could be convinced, but given this seems to be going against the tide of prevailing thought by other taxonomic bodies I will wait and see.

I'd been on the fence on whether Sternidae and Pluvianellidae warrant family status, so I am happy to see TiF agree with my own gut instincts for both groups. I do also find it interesting that while they haven't gone through with it, TiF is also in a "wait and see" situation on whether or not Scolopacidae should be split up into multiple families or whether oystercatchers and stilts/avocets deserve to be a single family. My gut tells both of those options are probably more correct, but I will let someone make that call first before updating my checlist

I don't buy noddies as being the sister group to gulls. Their doesn't seem to be strong support for either a closer relationship with Sternidae or a closer relationship with Laridae (or possibly being sister to both). Even the authors of the paper responsible for many of these changes highlight this as an unstable part of the tree where more work is needed. If I was a betting man I would place money on these being closer to Sternidae than to Laridae.
 
Mysticete said:
Not sure I feel comfortable splitting apart Calidris. While in theory I don't mind cryptic genera, to me the degree of morphological similarity makes me question the merit of finely splitting apart the genus as currently recognized. I could be convinced, but given this seems to be going against the tide of prevailing thought by other taxonomic bodies I will wait and see.
Click to expand...

Can the maintenance of a single genus which includes Ruff, Surfbird, Curlew Sandpiper, Buff-breasted Sandpiper and Spoon-billed Sandpiper, amongst other disparate forms, really be justified by arguments of morphological similarity?

I'm similarly unpersuaded by arguments for a broad Calidris in terms of "nomenclatural stability" - in that most traditional Calidris will remain so. I can't get behind any taxonomy which does not treat Ruff in a monospecific genus!

In my personal list, I recognise the following:

Erolia himantopus/ferruginea

Eurynorhynchus subminutus/temminckii/ruficollis/pygmeus

Pelidna alba/alpina/ptilocnemis/maritima

Ereunetes bairdii/fuscicollis/minutillus/minutus/pusillus/mauri/melanotos

Tryngites subruficollis

Philomachus pugnax

Limicola acuminata/falcinellus
 
andrew147 said:
Can the maintenance of a single genus which includes Ruff, Surfbird, Curlew Sandpiper, Buff-breasted Sandpiper and Spoon-billed Sandpiper, amongst other disparate forms, really be justified by arguments of morphological similarity?
Click to expand...

On the other hand, breaking up Calidris results in some arrangements that are hard to fathom. At least as a field birder, it's hard to believe that Least Sandpiper and Long-toed Stint are in separate genera, same for Semipalmated Sandpiper and Red-necked Stint. Sharp-tailed Sandpiper being sister to Broad-billed, and in a separate genus from Pectoral, is another suprising result.

Plus you'd have to change the title of what to me remains the greatest field identification article ever published: https://sora.unm.edu/sites/default/files/journals/nab/v038n05/p00853-p00876.pdf
 
cajanuma said:
On the other hand, breaking up Calidris results in some arrangements that are hard to fathom. At least as a field birder, it's hard to believe that Least Sandpiper and Long-toed Stint are in separate genera, same for Semipalmated Sandpiper and Red-necked Stint. Sharp-tailed Sandpiper being sister to Broad-billed, and in a separate genus from Pectoral, is another suprising result.

Plus you'd have to change the title of what to me remains the greatest field identification article ever published: https://sora.unm.edu/sites/default/files/journals/nab/v038n05/p00853-p00876.pdf
Click to expand...
I don't disagree with what you are saying - if the genetics are correct, there's some serious morphological conservatism going on in this group, though some of the less convincing details may be refined with more studies. But, for me, a broad Calidris is too heterogeneous and something as morphologically and behaviourally idiosyncratic as Ruff should not have been taken out of a monospecific genus - especially when this is supported by divergence time estimates (Černý and Natale (2021) have it as an isolated lineage for 19 million years). And if you start with a monospecific Philomachus, then, based on current understanding, the remainder must be carved up something akin to the genera I outlined above - though other genera could also be recognised (e. g. Micropalama, Leimonites, Crocethia).

Ultimately though, it does come down to personal preference - we're not all gonna agree and the differences in opinion make for interesting discussion.

And that is a great article, thanks!
 
Last edited:
Calidris canutus

Yvonne I Verkuil, Erika Tavares, Patricia M González, Kristen Choffe, Oliver Haddrath, Mark Peck, Lawrence J Niles, Allan J Baker, Theunis Piersma, and Jesse R Conklin. Genetic structure in the nonbreeding range of rufa Red Knots suggests distinct Arctic breeding populations. Ornithological Applications, Published: 20 November 2021.
https://doi.org/10.1093/ornithapp/duab053

Abstract
An understanding of the migratory connectivity between breeding and nonbreeding areas is fundamental to the management of long-distance migrants under pressure from habitat change along their flyways. Here we describe evidence for genetic structure within the nonbreeding range of the endangered Arctic-Canadian rufa subspecies of Red Knots (Calidris canutus). Using blood and tissue samples from the major nonbreeding regions in Argentina (Tierra del Fuego and Río Negro), northern Brazil (Maranhão), and southeastern USA (Florida), we estimated genetic structure in 514 amplified fragment length polymorphism (AFLP) loci, applying cluster assignment analyses in DAPC, assignPOP, and STRUCTURE. Using a priori location information, individuals could be correctly re-assigned to their nonbreeding regions, which validated that the assignment accuracy of the data was sufficient. Without using a priori location information, we detected 3–5 genotype clusters, and posterior assignment probabilities of samples to these genotype clusters varied among the three regions. Lastly a chi-square test confirmed that allele frequencies varied significantly among nonbreeding regions, rejecting the hypothesis that samples were drawn from a single gene pool. Our findings hint at undescribed structure within the Red Knot rufa breeding range in the Canadian Arctic and indicate that each rufa nonbreeding area in this study hosts a different subsample of these breeding populations. The observation that nonbreeding sites of rufa Red Knots contain different genetic pools argues for separate conservation management of these sites.
 
Päckert, Martin. Free access of published DNA sequences facilitates regular control of (meta-) data quality – an example from shorebird mitogenomes (Aves, Charadriiformes: Charadrius). Ibis.
https:doi.org/10.1111/ibi.13005

Abstract
Online repositories of DNA sequences are a rich and indispensable source of comparative data for biodiversity research and taxonomic studies. Despite increasingly high data quality of published sequences and associated metadata, particular attention should be paid to taxonomic assignment of DNA sequences, in particular if voucher specimens are not available or cannot be examined. In this study, two nearly identical mitogenomes of two distinctive plover species (Charadrius alexandrinus and Charadrius placidus) were re-analysed and compared with a comprehensive dataset of DNA-barcode sequences (cytochrome-oxidase subunit 1, COI) for 55 shorebird species. Phylogenetic analysis separated the two plover species into two reciprocally monophyletic clades that differed by mean p-distances of 11.5–14.7%; however, the COI sequence from the C. placidus mitogenome was nested in the Kentish Plover clade (C. alexandrinus). A similar mismatch was found for another DNA-barcode sequence from a Charadrius mongolus mitogenome that clustered with one of two clades of Charadrius leschenaultii in the COI tree. These results strongly suggest that, to date, two of seven mitogenomes published for Charadriidae are not representative of the taxon names to which the respective GenBank entries were assigned. Only a few DNA-barcode sequences were associated with outdated taxonomy, while others were suspected to be chimeric sequences. Thus, free access to digital sequence information is a key factor for steady improvement of data quality in online repositories via swarm intelligence of the scientific community.
 
This makes a lot of sense, I'm glad someone has taken a dive into Charadrius because I don't think anyone here believes the current tree for this group is correct.
 
Still some weird stuff going on
Placement of veredus for example seems very unexpected?... so far from leschenaulti and mongola
Anyway, good to see work done on Charadrius
 
For Long-billed Plover:
The mitogenome KY419888 is indeed clearly C. alexandrinus.
Of the four available cox1 sequences: KM001301, KM001302, and KM001303 are almost identical to one another (0 to 1 substitution in 429 bp), and differ from MT602072 almost exclusively in their central parts (e.g., KM001301 vs. MT602072: 26 substitutions, all of them between bp 130 and 310). Martin Päckert also noted this, and used it to discard MT602072, suggesting that it "might also be due to a sequencing artefact". However, the central parts of KM001301-3 are all nearly identical to (differ at most by one substitution from) KM001260, KM001261, KM001262, FJ027337, FJ027338, FJ027339, FJ027340, FJ027341, BROM480-07, and BROM481-07, which are all C. alticola and all have flanking parts that differ strongly from those of KM001301-3. The only plausible interpretation I can see is that the three sequences KM001301-3 are chimeric (have a central part that comes from C. alticola) -- instead of MT602072, which may thus well be OK.
Thus I do not believe the position of this species in Martin Päckert's tree is correct.

(As a consequence of the above, the relationships within the rest of the CRD II clade in this tree, with the C. alticola / falklandicus group basal in the group to which the C. placidus chimeric sequences are sister, should be regarded with extreme caution as well. The alticola part of the chimeras will have attracted the pure C. alticola towards them, which may have altered the relationships within this clade (i.e., have moved alticola / falklandicus to a spuriously basal position), or its rooting (i.e., have changed the orientation of the clade, without necessarily affecting the network of relationships linking its constituents).)
 
Last edited:
The take home message is that essentially we need to burnt it all to the ground and start again. The other bit of clear nonsense in this group is the current positioning of forbesi to tricollaris.

My research is currently focused on shorebirds, with a particular focus on some Charadrius species. I have been pushing for a new look at this with some of my colleagues and hopefully we can do a resampling drive!

I can reveal that there should be one or two papers of interest to this subforum from Charadrius species this year. Watch this space!
 
Jacana said:
The other bit of clear nonsense in this group is the current positioning of forbesi to tricollaris.
Click to expand...

forbesi is part of a group that also includes tricollaris, cucullatus, melanops, novaeseelandiae, dubius, placidus (not the chimeras), and the hiaticula-melodus-semipalmatus-vociferus clade. I think going beyond this amounts to over-reading the data that are available at this point. (The only things we have for this species are a 429-bp fragment of cox1, which gives no significant resolution of the relationships within the group, and a 210-bp fragment of myo which is fully identical to that found in tricollaris and novaeseelandiae (and has not been sequenced for melanops and placidus). I see nothing in this that contradicts, in particular, a sister-group relationship between forbesi and tricollaris.)

What I have gathered from playing with GenBank data, is an general inclination not to be confident about anything that has not been found several times independently. I often prefer to see things that have already been done being repeated (by other researchers, in other facilities, using other specimens), to validate or invalidate earlier data, rather than having earlier data blanketly displaced by new data of a different nature, for which no independent validation may be available either...
But, anyway, I'll be among those who'll be watching. ;)
 
Last edited:
Jacana said:
The take home message is that essentially we need to burnt it all to the ground and start again. The other bit of clear nonsense in this group is the current positioning of forbesi to tricollaris.

My research is currently focused on shorebirds, with a particular focus on some Charadrius species. I have been pushing for a new look at this with some of my colleagues and hopefully we can do a resampling drive!

I can reveal that there should be one or two papers of interest to this subforum from Charadrius species this year. Watch this space!
Click to expand...
And I hope that you will not forget to have a look on the apparently overlumped genus Vanellus which has been neglected much too long.
 

Users who are viewing this thread

Total: 2 (members: 0, guests: 2)
Back
Top